Sequencing Documentation

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Description
 
File Info
Date
AmpliSeq for Illumina Comprehensive Cancer Panel Checklist

This checklist is a condensed form of the AmpliSeq for Illumina Comprehensive Cancer Panel protocol. It is easy to print and carry with you in the lab.

HiSeq X Software v3.3.39 Release Notes

This document describes the changes and features introduced in HiSeq X software package v3.3.39, which includes HiSeq X Control Software v3.3.39 and updates to RTA, recipes, the BaseSpace Broker, and Sequencing Analysis Viewer software.

TruSeq Stranded mRNA Library Prep for NeoPrep Checklist

This checklist is a condensed form of the TruSeq Stranded mRNA Library Prep for NeoPrep protocol. It is easy to print and carry with you in the lab.

ScriptSeq Complete (Human/Mouse/Rat) Low-Input Library Prep Guide

This guide provides instructions for preparing sequencing libraries using the ScriptSeq Complete (Human/Mouse/Rat) Low-Input Kit.

AmpliSeq for Illumina Cancer HotSpot Panel v2 Checklist

This checklist is a condensed form of the AmpliSeq for Illumina Cancer HotSpot Panel v2 protocol. It is easy to print and carry with you in the lab.

SurePlex Summary Protocol Reference Guide
Experienced-level instructions for preparing samples using the SurePlex DNA Amplification kit.
HiSeq 3000 System Guide

The system guide describes instrument components, on-instrument software, the sequencing workflow, and maintenance procedures for the HiSeq 3000.

TruSeq Stranded mRNA Sample Prep HS EUC and LTF

Experienced-level instructions for preparing samples using the HS protocol for the TruSeq Stranded mRNA Sample Prep Kit.

TruSeq RNA Sample Preparation v2 High Sample Experienced User Card and Lab Tracking Form

Experienced-level instructions for preparing samples using the high sample protocol for the TruSeq RNA Sample Preparation v2 Kit.

NextSeq System Custom Primers Guide

This guide contains instructions for using custom primers on the NextSeq 500 and NextSeq 550 systems, which includes preparing and loading primers, and setting up the run to specify custom primers for the run.

AmpliSeq for Illumina Transcriptome Human Gene Expression Panel Reference Guide

This guide contains everything a first-time user needs, including an overview of the AmpliSeq for Illumina Transcriptome Human Gene Expression Panel protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

MiniSeq System Guide

This guide contains an overview of instrument components and instructions for operating and maintaining the MiniSeq System.

TruSight Tumor Sample Prep Experienced User Card

Intended for the experienced user, this document summarizes instructions for using the TruSight Tumor Sample Prep Kit. Sufficient reagents are supplied for 48 samples and indexes provided enable sample indexing of 4 samples per sequencing run.

HiSeq Upgrade Welcome Letter

This is the welcome letter that was sent to customers about their HiSeq upgrade.

MiSeq Sequencing Welcome Card

This quick reference card is a graphical introduction to the MiSeq instrument. It covers information such as MiSeq appllications, MiSeq publications, Sample Preparation, navigating through the support website, and MiSeq community resources.

Nextera DNA Flex Microbial Colony Extraction Protocol Guide

Instructions for preparing samples from bacteria colonies.

Installing MiSeq Reporter on an Off-Instrument Computer (15031742)

 

For instructions on how to install MiSeq Reporter software off-instrument, see the MiSeq Reporter Software Guide.

TruSeq Targeted RNA BaseSpace App Documentation

For instructions on using the TruSeq Targeted RNA BaseSpace App, see TruSeq Targeted RNA v1.0 Online Help.

Nextera Enrichment Sample Preparation Guide

Instructions for preparing samples using the Nextera Enrichment sample prep Kit.

mRNA-Seq Sample Prep Guide (1004898 D)

This download contains the sample preparation guide for mRNA sequencing.

Read 1 Primer Rehybridization on a HiSeq X Flow Cell

Instructions for performing Read 1 primer rehybridization on a HiSeq X flow cell using the cBot.

Directional mRNA-Seq Sample Prep Guide (15018460)

Instructions for performing the Directional mRNA-Seq sample prep assay.

Mate Pair Library v2 Sample Preparation Guide for 2-5 kb Libraries (15008135)

Instructions for preparing samples using the Mate Pair Library Kit v2.

AmpliSeq for Illumina Comprehensive Cancer Panel Reference Guide

This guide contains everything a first-time user needs, including an overview of the AmpliSeq for Illumina Comprehensive Cancer Panel protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

TruSeq Small RNA Library Prep Experienced User Card

Experienced-level instructions for the TruSeq Small RNA Library Prep Kit.

HiSeq v4 System Upgrade FAQ

This document describes key upgrade features, upgrade components, software upgrade features, and new chemistry features.

Illumina Adapter Sequences Document

This document contains oligonucleotide (oligo) sequences of Illumina adapters used in Nextera, TruSeq, TruSight, and AmpliSeq for Illumina library prep kits. This information is provided for use with Illumina sequencing instruments only: MiSeq, NextSeq, and HiSeq systems.

HiSeq Systems Denature and Dilute Libraries Guide

This guide contains instructions for denaturing and diluting libraries after library preparation and before sequencing on a HiSeq system. This guide also includes instructions for preparing a PhiX control.

ForenSeq DNA Signature Prep Protocol Guide

This guide contains just the steps needed to prepare ForenSeq DNA Signature Prep libraries. It is intended for users who are experienced with Illumina library prep methods.

Genome Analyzer IIx Run Rescue Protocols (15019044)

Instructions for restoring failed runs on the Genome Analyzer.

MiSeq Reagent Kit What's New Insert

Overview of changes introduced with the MiSeq reagent kit versions, related documentation, and software requirements.

NextSeq 550Dx Research Mode Instrument Reference Guide

Instructions for using the NextSeq 550Dx instrument in research (RUO) mode.

HiSeq 1500 System Guide

This guide provides an overview of instrument components and instructions for operating and maintaining the HiSeq 1500. Workflows include HiSeq v4, TruSeq v3, and Rapid Run.

TruSeq Stranded Total RNA Sample Prep Guide

Instructions for preparing samples using the TruSeq Stranded Total RNA Sample Prep Kit.

TruSeq Stranded Total RNA is also offered in the following configuration. Refer to TruSeq Stranded Total RNA if you have ordered product 20020596, 20020597, 20020598, 20020599, 20020610, 20020611, 20020612, or 20020613.

TruSeq Custom Amplicon Low Input Kit Reference Guide

This guide contains everything a first-time user needs, including an overview of the TruSeq Custom Amplicon Low Input Kit protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

NovaSeq 6000 Sequencing System Guide

This guide provides an overview of instrument components and instructions for operating and maintaining the NovaSeq 6000 Sequencing System.

MiSeqDx Cystic Fibrosis 139-Variant Assay Physician Insert

This insert contains physician information for the MiSeqDx Cystic Fibrosis 139-Variant Assay.

MiSeq Reporter TruSight Tumor 15 Workflow Guide

This guide provides an overview of the MiSeq Reporter TruSight Tumor 15 analysis workflow, including installation instructions, workflow requirements, and descriptions of analysis output files.

TruSeq RNA Sample Preparation High Throughput Lab Tracking Form

Instructions for using the TruSeq RNA sample prep HT protocol.

Nextera Rapid Capture Enrichment User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the Nextera Rapid Capture Enrichment Guide.

GenomeStudio RNA Sequencing Module v1.0 User Guide (11319105)

Instructions for using the GenomeStudio RNA Sequencing Module v1.0 to view sequencing data.

AmpliSeq for Illumina Comprehensive Cancer Panel Consumables & Equipment

Consumables and equipment used with the AmpliSeq for Illumina Comprehensive Cancer Panel. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window.

Using Custom Primers on the MiSeq

This guide provides instructions for using custom primers for sequencing on the MiSeq.

MiSeq FGx Instrument Safety and Compliance Guide

 

This guide contains safety information and product compliance markings for the MiSeq FGx Instrument.

 

BaseSpace Variant Interpreter Online Help

For instructions on using BaseSpace Interpreter, visit BaseSpace Variant Interpreter Online Help.

Nextera Flex for Enrichment Reference Guide

Consumables and equipment used with the Nextera Flex for Enrichment protocol. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window.

Whole Genome Sequencing BaseSpace App Documentation

For instructions on using the Whole Genome Sequencing BaseSpace App, see the Whole Genome Sequencing v8.0 Online Help.

NextSeq System Site Prep Guide

This guide contains lab specifications and requirements for preparing a site for the NextSeq 500 and NextSeq 550 systems.

FastTrack Services Long Reads Pipeline User Guide

This document provides an overview of the Long Read Sequencing Service informatics pipeline. It provides details of the source and contents of the main files that Illumina sequencing services creates when assembling long read data sets. Additionally it provides information about the algorithms used for assembling the synthetic long reads. The aim of this document is to help you understand the Long Read Sequencing Service data package that you received from Illumina.

TruSeq DNA Sample Preparation Low Sample Experienced User Card

Experienced-level instructions for using the TruSeq DNA sample prep LS protocol.

TruSeq DNA Sample Preparation High Sample Experienced User Card

Experienced-level instructions for using the TruSeq DNA sample prep HS protocol.

TG NextSeq 500 High Output Kit Documentation

For information about the TG NextSeq 500 High Output Kit, see Contents & Storage and Requirements & Compatibility. For preparation instructions, see the NextSeq 500 System Guide.

Read 1 Primer Rehybridization on a HiSeq 3000/4000 Flow Cell

Instructions for performing Read 1 primer rehybridization on a HiSeq 3000/4000 flow cell using the cBot.

Preparing Samples for Paired-End Sequencing (1005063)

Instructions for preparing samples using the Paired-End sample prep Kit.

TruSeq Synthetic Long-Read DNA Library Prep Sequencing and Analysis Product Insert

This document outlines sequencing and analysis workflows with the TruSeq Synthetic Long-Read DNA Library Prep and TruSeq Synthetic Long-Read DNA Barcode kits.

ScriptSeq Complete (Plant Seed/Root) Library Prep Guide

This guide provides instructions for preparing sequencing libraries using the ScriptSeq Complete (Plant Seed/Root) Kit.

TruSeq DNA Sample Preparation High Sample Lab Tracking Form

Lab tracking form for the TruSeq DNA sample prep HS protocol.

NovaSeq Series Safety and Compliance Guide

This guide describes safety information and provides product compliance statements for the NovaSeq Series of Sequencing Systems.

MiSeq Reporter Workflows in BaseSpace Customer Release Notes

Release notes for MiSeq Reporter workflows in BaseSpace.

Nextera Rapid Capture Enrichment Protocol Guide

This guide contains just the steps needed to prepare Nextera Rapid Capture enriched libraries. It is intended for users who are experienced with Illumina library prep methods.

AmpliSeq for Illumina BRCA Panel Consumables & Equipment

Consumables and equipment used with the AmpliSeq for Illumina BRCA Panel. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window.

HiSeq System Upgrade Information Sheet

This document describes key upgrade features, upgrade components, software upgrade features, and new chemistry features.

TruSeq Small RNA Library Prep Kit Protocol Guide

This guide contains just the steps needed to prepare TruSeq Small RNA libraries. It is intended for users who are experienced with Illumina library prep methods.

Off-Line Basecaller v1.9.4 User Guide (15009920)

Instructions for using OLB v1.9.4 for basecalling and converting *.bcl files to *qseq.txt files.

AmpliSeq for Illumina Immune Response Panel Consumables & Equipment

Consumables and equipment used with the AmpliSeq for Illumina Immune Response Panel. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window.

Excerpt (Troubleshooting) from HiScanSQ System User Guide (15015392)

Instructions for troubleshooting problems on the HiScanSQ.

TruSeq Stranded Total RNA Sample Preparation User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq Stranded Total RNA Sample Preparation Guide.

TruSeq RNA Sample Preparation Guide

This download contains the guide for the TruSeq RNA Sample Preparation protocol for sequencing.

TruSeq Stranded mRNA Library Prep for NeoPrep User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq Stranded mRNA Library Prep for NeoPrep Reference Guide.

TruSight Enrichment DNA Sample Prep Kit Lab Tracking Form

This download contains the lab tracking form for the TruSight Enrichment DNA Sample Prep Kit.

MiSeq Sample Sheet Quick Reference Guide

This guide provides guidance for setting up sample sheets for sequencing on the MiSeq.

TruSeq Targeted RNA Expression Experienced User Card

 

Experienced-level instructions for preparing libraries using the TruSeq Targeted RNA Expression Kit.

 

BlueFuse Multi Walkthrough Guides
This document provides links to video walkthrough guides to assist with using BlueFuse Multi Software.
16S Metagenomic Sequencing Library Preparation

Includes the 16S Illumina Demonstrated Library Prep Guide and links to an example 16S dataset from libraries generated with the protocol and run on the MiSeq with v3 reagents.

TruSight Tumor 26 Protocol Guide

This guide contains just the steps for the TruSight Tumor 26 protocol. It is intended for users who are experienced with Illumina library prep methods.

RRBS for Methylation Analysis Guide

Instructions for RRBS for Methylation Analysis.

Primer Rehybridization on a HiSeq High Output Flow Cell

This guide contains instructions for performing primer rehybridization on the HiSeq using the HiSeq Multi-Primer Rehyb Kit v4. Instructions for a TruSeq v3 Read 2 primer rehybridization are also included.

CASAVA v1.8.2 Quick Reference Guide (15011197 C)

This download contains the quick reference guide for CASAVA v1.8.2 sequencing analysis software.

TG VeriSeq NIPT Solution Consumables & Equipment
Consumables and equipment used with the TG VeriSeq NIPT Solution. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window.
TruSeq Small RNA Library Prep User-Supplied Consumables and Equipment

 

Consumables and equipment excerpt from the TruSeq Small RNA Library Prep Guide.

 

Nextera Mate Pair Sample Preparation Guide

This guide explains how to prepare samples using the Nextera Mate Pair Sample Preparation Kit.

CASAVA v1.8 Quick Reference Booklet (15011197 B)

This download contains the quick reference booklet for CASAVA v1.8 sequencing analysis software.

HiSeq Rapid SBS Kit v2 Reference Guide

For information about the HiSeq Rapid SBS Kit v2, see Contents & Storage and Requirements & Compatibility. For preparation instructions, see the HiSeq 2500 System Guide or the HiSeq 1500 System Guide.

TruSeq Synthetic Long-Read DNA Library Prep User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq Synthetic Long-Read DNA Library Prep Guide.

Nextera XT DNA Library Prep Kit Consumables & Equipment List

This document lists the consumables and equipment used with the Nextera XT DNA Library Prep Kit.

IEM TruSight Quick Reference Card

Instructions for using IEM with TruSight kits.

Local Run Manager Amplicon DS Analysis Module Workflow Guide

This guide provides instructions for setting up a run and viewing analysis results using the Amplicon DS analysis module.

TruSeq Nano DNA Library Prep for NeoPrep User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq Nano DNA Library Prep for NeoPrep Reference Guide.

bcl2fastq Conversion Software v1.8.4 User Guide

This guide includes instructions for using the bcl2fastq Conversion Software v1.8.4 to demultiplex data and convert BCL files from MiSeq or HiSeq systems running RTA versions earlier than 1.8 to standard FASTQ file formats for downstream analysis.

ScriptSeq Complete Gold (Epidemiology) Library Prep Guide

This guide provides instructions for preparing sequencing libraries using the ScriptSeq Complete Gold (Epidemiology) Kit.

TruSeq Targeted RNA Expression Guide

 

Instructions for preparing libraries using the TruSeq Targeted RNA Expression Kit.

 

TruSeq RNA Sample Preparation v2 Low Sample Experienced User Card and Lab Tracking Form

Experienced-level instructions for preparing samples using the low sample protocol for the TruSeq RNA Sample Preparation v2 Kit.

HiScanSQ Pausing a Sequencing Run to Scan BeadChips (15023459 A)

Instructions for pausing a sequencing run on the HiScanSQ.

Local Run Manager for MiniSeq Software Guide

This guide provides an overview of the Local Run Manager software, instructions for using software features, and instructions for installing analysis modules on the instrument computer.

MiSeqDx Instrument Site Preparation Guide

This guide provides requirements for preparing a lab for the MiSeqDx Platform: lab space requirements, electrical requirements, bench recommendations, UPS recommendations, and user-supplied consumables. For customers that do not have a MiSeqDx instrument with dual boot upgrade. If you are not sure if your instrument has the dual boot upgrade, contact Illumina Technical Support.

Lab Tracking Form Single-Read Cluster Station v5 (15019439)

Lab Tracking Form Single-Read Cluster Station v5 (15019439)

TruSeq Ribo Profile Index Primers Guide

This guide provides instructions for using index primers with the TruSeq Ribo Profile (Yeast) and TruSeq Ribo Profile (Mammalian) library prep kits.

CASAVA User Guide (15011196 D)

This download contains the user guide for the CASAVA sequencing analysis software.

Frequently Asked Questions (FAQs) - Certificate of Analysis (CofA)

Frequently Asked Questions (FAQs) for the Certificate of Analysis (CofA)

NextSeq 500 Kit v1 Documentation

For information about the NextSeq 500 Kit (v1), see Contents & Storage and Requirements & Compatibility. For preparation instructions, see the NextSeq 500 System Guide and Additional Setup Step for NextSeq 500 Kit v1.

TruSeq DNA Sample Preparation User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq DNA Sample Preparation Guide.

CASAVA Software Version 1.7 User Guide (15011196 A)

This download contains the user guide for the CASAVA v1.7 sequencing analysis software.

Local Run Manager Amplicon DS Analysis Module Workflow Guide

This guide provides instructions for setting up a run and viewing analysis results using the Amplicon DS analysis module.

TruSeq Custom Amplicon Low Input Library Prep Protocol Guide

This guide contains just the steps needed to prepare TruSeq Custom Amplicon Low Input libraries. It is intended for users who are experienced with Illumina library prep methods.

HiSeq 4000 and HiSeq 3000 Systems Safety and Compliance Guide

The safety and compliance guide describes safety considerations and lists product compliance markings for the HiSeq 4000 and HiSeq 3000.

Local Run Manager Software Reference Guide for MiSeqDx

An overview of the Local Run Manager software for MiSeqDx, and instructions for using software features.

Nextera DNA Flex Metagenomics Lysate Protocol Guide

Instructions for preparing crude lysate from bacterial culture and stool samples.

MiSeqDx Site Preparation Guide for Instruments with Dual Boot Configuration

For customers that have a MiSeqDx instrument with dual boot upgrade. If you are not sure if your instrument has the dual boot upgrade, contact Illumina Technical Support. This guide provides requirements for preparing a lab for the MiSeqDx Platform: lab space requirements, electrical requirements, bench recommendations, UPS recommendations, and user-supplied consumables. 

Enrichment BaseSpace App Documentation

For instructions on using the Enrichment BaseSpace App, see Enrichment v3.1 Online Help.

MethylSeq BaseSpace App Documentation

For instructions on using the MethylSeq BaseSpace App, see MethylSeq v1.0 Online Help.

MiSeq FGx Instrument Reference Guide

 

This guide includes information about instrument components, MiSeq FGx Control Software, and required consumables, and instructions for performing a sequencing run and maintaining the instrument.

 

Index Adapters Pooling Guide

The Index Adapters Pooling Guide provides guidelines for preparing libraries with balanced index combinations for sequencing on Illumina systems. This guide replaces the TruSeq Library Prep Pooling Guide (document # 15042173) and the Nextera Low Plex Pooling Guidelines (Pub. No. 770-2011-044).

TruSight Tumor 15 Consumables and Equipment

Consumables and equipment used with the TruSight Tumor 15 Kit. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window

MiSeqDx Reference Guide for Instruments with Dual Boot Configuration

For customers that have a MiSeqDx instrument with dual boot upgrade. If you are not sure if your instrument has the dual boot upgrade, contact Illumina Technical Support. This guide includes information about instrument components, MiSeq Operating Software, and instructions for performing a sequencing run and maintaining the MiSeqDx instrument. 

TruSeq Rapid Exome Library Prep Reference Guide

This guide contains everything a first-time user needs, including an overview of the TruSeq Rapid Exome Library Prep protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

TruSeq DNA Sample Preparation (v1) High Throughput Lab Tracking Form

Lab tracking form for the TruSeq DNA sample prep HT assay.

Human_mtDNA_D_Loop_Hypervariable_Region Guide (15034858)

Instructions for Human mtDNA D-Loop Hypervariable Region sample preparation.

BaseSpace Core App End-User License Agreements.

 

End-User License Agreements (EULAs) for BaseSpace Core App.

 

NextSeq System Safety and Compliance Guides

The safety and compliance guide contains safety considerations and product compliance markings for the NextSeq 500 and NextSeq 550 systems.

The RFID Reader guide contains compliance information for the RFID reader, an internal component of the NextSeq 500 and NextSeq 550 systems.

MiSeqDx Cystic Fibrosis Clinical Sequencing Assay Reference Guide

This guide contains best practices and instructions for preparing libraries using the MiSeqDx Cystic Fibrosis Clinical Sequencing Assay.

Paired-End Cluster Generation Lab Tracking Form (15009438)

This download contains the interactive lab tracking form for paired-end cluster generation on the Cluster Station.

TruSight RNA Pan-Cancer Panel Consumables & Equipment

Consumables and equipment used with the TruSight Pan-Cancer Panel. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window.

Nextera DNA Flex Library Prep Checklist

This checklist is a condensed form of the Nextera DNA Flex protocol. It is easy to print and carry with you in the lab.

TruSight HLA Sequencing Panel Reference Guide

This guide contains everything a first-time user needs, including an overview of the TruSight HLA protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

TruSeq SBS Kit v3 Reagent Prep Guide

For information about the TruSeq SBS Kit v3, see Contents & Storage and Requirements & Compatibility. For preparation instructions, see the HiSeq 2500 System Guide, the HiSeq 1500 System Guide, or the HiSeq 2000 System Guide.

Local Run Manager Software Guide

This guide provides an overview of the Local Run Manager software, instructions for using software features, and instructions for installing analysis modules on the instrument computer.

RFID Reader Module Compliance Guide

Compliance statements for the RFID Reader (Model # TR-001-44), an internal component of the NextSeq 550Dx System.

AmpliSeq for Illumina Cancer HotSpot Panel v2 Reference Guide

This guide contains everything a first-time user needs, including an overview of the AmpliSeq for Illumina Cancer HotSpot Panel v2 protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

TruSeq Rapid Duo cBot Sample Loading Kit Reagent Prep Guide

For information about the HiSeq Rapid Duo cBot Sample Loading Kit, see Contents & Storage and Requirements & Compatibility. For preparation instructions, see the cBot System Guide.

VeriSeq NIPT Analysis Software (48 Samples) Guide

Instructions for analyzing NGS data using the VeriSeq NIPT Analysis Software (48 Samples).

TruSight Tumor 15 Checklist

This checklist is a condensed form of the TruSight Tumor 15 protocol. It is easy to print and carry with you in the lab.

TruSeq Nano DNA Library Prep Protocol Guide

This guide contains just the steps needed to prepare TruSeq Nano DNA libraries. It is intended for users who are experienced with Illumina library prep methods.

iSeq 100 Sequencing System Safety and Compliance Guide

The safety and compliance guide provides important safety information pertaining to the installation, servicing, and operation of the iSeq 100 Sequencing System and includes product compliance and regulatory statements.

AmpliSeq for Illumina Focus Panel Consumables & Equipment

Consumables and equipment used with the AmpliSeq for Illumina Focus Panel. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window.

RNA-Seq Alignment App Documentation

For instructions on using the RNA-Seq Alignment BaseSpace App, see RNA-Seq Alignment v1.0 Online Help.

TruSeq Custom Amplicon Library Preparation Guide

Instructions for preparing samples using the TruSeq Custom Amplicon Library Preparation Kit.

cBot System Site Prep Guide

This guide contains lab specifications and requirements for preparing a site for the cBot 2 and cBot systems.

AmpliSeq for Illumina Direct FFPE DNA Kit Reference Guide

This guide contains everything a first-time user needs, including an overview of the AmpliSeq for Illumina Direct FFPE DNA Kit protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

TruSight RNA Pan-Cancer Panel Checklist

This checklist is a condensed form of the TruSight RNA Pan-Cancer Panel protocol. It is easy to print and carry with you in the lab.

Nextera DNA Sample Preparation Lab Tracking Form

Interactive form for recording sample preparation steps using the Nextera DNA sample prep Kit.

HiSeq 3000/4000 SBS Kit Information

For information about the HiSeq 3000/4000 SBS Kit, see Contents & Storage and Requirements & Compatibility. For preparation instructions, see the HiSeq 4000 System Guide or the HiSeq 3000 System Guide.

MiSeqDx Cystic Fibrosis 139-Variant Assay Local Run Manager Guide

Instructions for setting up a run and viewing analysis results using the CF 139 Variant analysis module.

Cluster Station Support - User Guide Download

Instructions for using the Cluster Station for cluster generation.

BaseSpace Sequence Hub Pro Workgroup Admin Quick Reference Card

Instructions for the BaseSpace Sequence Hub Pro Workgroup Administrator.

Nextera Mate Pair Gel-Free Experienced User Card

Intended for the experienced user, this document summarizes the steps for preparing samples using the Nextera Mate Pair Gel-Free protocol.

TruSeq Nano DNA Library Prep for NeoPrep Checklist

This checklist is a condensed form of the TruSeq Nano DNA Library Prep for NeoPrep protocol. It is easy to print and carry with you in the lab.

TruSeq Stranded mRNA Dual Index Product Insert

Instructions for dual-indexing with TruSeq Stranded mRNA HT Sample Prep.

TruSight Rapid Capture Sample Prep Experienced User Card

Intended for the experienced user, this document summarizes instructions for using the TruSight Rapid Capture Sample Prep Kit to prepare up to 96 indexed paired-end libraries, followed by enrichment using the TruSight Content Set CSO (custom selected oligos).

TruSeq Stranded Total RNA Sample Prep HS EUC and LTF

Experienced-level instructions for preparing samples using the HS protocol for the TruSeq Stranded Total RNA Sample Prep Kit.

TruSight DNA Amplicon Library Preparation Guide

Instructions for preparing samples using the TruSight DNA Amplicon Library Preparation Kit.

TruSeq Rapid SBS Kit Reagent Prep Guide

For information about the TruSeq Rapid SBS Kit, see Contents & Storage and Requirements & Compatibility. For preparation instructions, see the HiSeq 2500 System Guide or the HiSeq 1500 System Guide.

AmpliSeq for Illumina Immune Repertoire Panel Reference Guide

This guide contains everything a first-time user needs, including an overview of the AmpliSeq for Illumina Immune Repertoire protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

TruSeq Nano DNA Library Prep Checklist

This checklist is a condensed form of the TruSeq Nano DNA Library Prep protocol. It is easy to print and carry with you in the lab.

IEM TruSeq or TruSight Amplicon Quick Reference Card

Instructions for using IEM with the TruSeq Amplicon or TruSight DNA Amplicon kits.

Ribo-Zero rRNA Removal Kit Reference Guide

This guide provides instructions for using the Ribo-Zero kits to remove rRNA from samples.

TruSight Enrichment DNA Sample Prep Guide

Instructions for using the TruSight Enrichment DNA Sample Prep Kit to prepare up to 96 indexed paired-end libraries, followed by enrichment using the TruSight Content Set CSO (custom selected oligos).

IEM SureCell WTA 3' Quick Reference Card

Instructions for using IEM  with the SureCell WTA 3' Kit.

TruSight Tumor Sample Prep Guide

Instructions for using the TruSight Tumor Sample Prep protocol.

MiSeqDx Cystic Fibrosis Assays Symbol Key

Explanations of symbols used in labeling for MiSeqDx Cystic Fibrosis Assays.

TruSeq RNA Sample Preparation Low Throughput Lab Tracking Form

Lab tracking form for the TruSeq RNA sample prep LT protocol.

Nextera DNA Sample Preparation Experienced User Card

Experienced-level instructions for preparing samples using the Nextera DNA sample preparation Kit.

MiSeq System Site Prep Guide

This guide provides requirements for preparing your lab for a MiSeq System: lab space requirements, electrical requirements, bench recommendations, UPS recommendations, and user-supplied consumables.

MiSeqDx Cystic Fibrosis Clinical Sequencing Assay Physician Insert

This document contains physician information for the MiSeqDx Cystic Fibrosis Clinical Sequencing Assay.

TruSight One Consumables and Equipment

This document provides a list of all of the necessary user-supplied consumables and equipment.

TruSight Tumor 15 BaseSpace App Documentation

For instructions on using the TruSight Tumor 15 BaseSpace App, see TruSight Tumor 15 v2.0.1 Online Help.

Conexio Assign v1.0 TruSight HLA Analysis Software User Guide

Instructions for using the Conexio Assign v1.0 TruSight HLA Analysis Software.

TruSight One Sequencing Panel Quick Reference Card

These application workflow card provide guidance for planning, running, and analyzing a TruSight One Sequencing Panel project.

AmpliSeq for Illumina Transcriptome Human Gene Expression Panel Checklist

This checklist is a condensed form of the AmpliSeq for Illumina Transcriptome Human Gene Expression Panel protocol. It is easy to print and carry with you in the lab.

TruSeq ChIP Sample Prep EUC and LTF

Experienced-level instructions for using the TruSeq ChIP Sample Prep Kit to prepare samples for sequencing.

iSeq 100 Sequencing System Setup Poster

The poster provides step-by-step instructions on how to install and set up the iSeq 100 Sequencing System.

Nextera XT DNA Sample Preparation Insert

Summary of the Nextera XT DNA sample preparation.

HiSeq Analysis Software v2.1 User Guide

This guide includes instructions for performing sequencing analysis using the HiSeq Analysis Software v2.1.

NextSeq 500 System Guide

This guide contains an overview of instrument components and instructions for operating and maintaining the NextSeq 500.

TruSeq Cluster Kit v2 (cBot-GA) Reagent Prep Guide

This guide contains descriptions of kit components and instructions for preparing reagents provided in TruSeq Cluster Kit v2.

NextSeq 550 System Guide

This guide contains an overview of instrument components and instructions for operating and maintaining the NextSeq 550.

TruSight Enrichment DNA Sample Prep Experienced User Card

Intended for the experienced user, this document summarizes instructions for using the TruSight Enrichment DNA Sample Prep Kit to prepare up to 96 indexed paired-end libraries, followed by enrichment using the TruSight Content Set CSO (custom selected oligos).

TruSeq Custom Amplicon Low Input Kit Consumables & Equipment List

This document lists the consumables and equipment used with the TruSeq Custom Amplicon Low Input Kit.

HiSeq 4000 System Guide

The system guide describes instrument components, on-instrument software, the sequencing workflow, and maintenance procedures for the HiSeq 4000.

Tumor Normal BaseSpace App Documentation

For instructions on using the Tumor Normal BaseSpace App, see Tumor Normal v6.0 Online Help.

AmpliSeq for Illumina Exome Panel Reference Guide

This guide contains everything a first-time user needs, including an overview of the AmpliSeq for Illumina Exome Panel protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

Ultra Low mRNA-Seq Sample Prep Guide

Instructions for Ultra Low mRNA-Seq sample preparation.

TruSight Tumor 26 Consumables and Equipment

Consumables and equipment used with the TruSight Tumor 26 Kit. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window

HiSeq 2500 System Safety and Compliance Guide

The safety and compliance guide describes safety considerations and lists product compliance markings for the HiSeq 2500 system.

Human mtDNA Genome Guide (15037958)

Instructions for Human mtDNA Genome sample preparation.

TruSeq Ribo Profile (Mammalian) Reference Guide

This guide contains an overview of the TruSeq Ribo Profile (Mammalian) protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables and equipment.

HiSeq X System Lab Setup and Site Prep Guide

The lab setup and site prep guide provides important information about setting up a lab for the HiSeq X Ten and HiSeq X Five systems, including instrument dimensions, lab space requirements, electrical requirements, user-supplied consumables, and storage space.

Genomic DNA Sample Prep Guide - Oligo Only Kit (1003492)

This download contains the sample preparation guide for sequencing genomic DNA (Oligo Only Kit).

BaseSpace Sequence Hub Data Storage Management Quick Reference Card

Instructions for managing data storage in BaseSpace Sequence Hub.

TruSeq DNA PCR-Free Library Prep Checklist

This checklist is a condensed form of the TruSeq DNA PCR-Free Library Prep protocol. It is easy to print and carry with you in the lab.

MiSeq Run Folder Quick Reference Card

Quick reference overview of the MiSeq Output and Analysis Folders.

TruSeq DNA Sample Preparation Low Sample Lab Tracking Form

Lab tracking form for the TruSeq DNA sample prep LS protocol.

Local Run Manager Somatic Variant Analysis Module Workflow Guide for NextSeq 550Dx

Instructions for setting up a run and viewing analysis results using the Somatic Variant analysis module for NextSeq 550Dx.

TruSight HLA Sequencing Panel Checklist

This checklist is a condensed form of the TruSight HLA protocol. It is easy to print and carry with you in the lab.

AmpliSeq for Illumina Exome Panel Checklist

This checklist is a condensed form of the AmpliSeq for Illumina Exome Panel protocol. It is easy to print and carry with you in the lab.

ScriptSeq Complete (Bacteria) Library Prep Guide

This guide provides instructions for preparing sequencing libraries using the ScriptSeq Complete (Bacteria) Kit.

IEM TruSeq DNA, RNA, or ChIP Quick Reference Card

Instructions for using IEM with the TruSeq DNA, RNA, or ChIP library prep kits.

MiSeqDx Instrument Reference Guide

This guide includes information about instrument components, MiSeq Operating Software, and instructions for performing a sequencing run and maintaining the MiSeqDx instrument. For customers that do not have a MiSeqDx instrument with dual boot upgrade. If you are not sure if your instrument has the dual boot upgrade, contact Illumina Technical Support.

MiSeqDx Cystic Fibrosis Clinical Sequencing Assay Lab Tracking Form

This document summarizes the steps in the MiSeqDx Cystic Fibrosis Clinical Sequencing Assay and includes fields for recording reagent lot numbers, as well as start and stop times for various steps.

Genome Analyzer IIx User Guide (for SCS v2.10) (15030966)

This guide contains an overview of instrument components and instructions for operating and maintaining the Genome Analyzer.

Genome Analyzer IIx Site Prep Guide

This guide contains lab specifications and requirements for installing and operating the Genome Analyzer.

BaseSpace Onsite Site Prep Guide

This guide contains site preparation instructions for the BaseSpace Onsite System, a genomics analysis platform that is a directly integrated end-to-end solution.

TruSight DNA Amplicon Library Preparation Experienced User Card

Experienced user level instructions for preparing samples using the TruSight DNA Amplicon Library Preparation Kit.

DesignStudio Customer Release Notes

DesignStudio release notes describe features and changes introduced in the latest versions of DesignStudio.

Nextera XT DNA Library Preparation Experienced User Card

Experienced-level instructions for preparing samples using the Nextera XT DNA library prep kit.

HiSeq X Lab Tracking Form

The lab tracking form is an interactive form for recording run details, reagent weights, and priming volumes.

Analysis Visual Controller v1.7 User Guide

Analysis Visual Controller (AVC) v1.7 User Guide

Local Run Manager Somatic Variant Analysis Module Workflow Guide for MiSeqDx

Instructions for setting up a run and viewing analysis results using the Somatic Variant analysis module for MiSeqDx.

NovaSeq Xp Workflow Checklist

This checklist provides high level steps for the NovaSeq Xp Workflow.

MiSeq Software Release Notes

MiSeq software release notes describe features and changes introduced in the latest versions of MiSeq Control Software (MCS) and related software components, including MiSeq Reporter.

TruSeq RNA Sample Preparation Low Throughput Experienced User Card

Experienced-level instructions for using the TruSeq RNA sample prep LT protocol.

iSeq 100 Sequencing System Site Prep Guide

The site prep guide provides lab specifications and requirements to prepare your site for the iSeq 100 Sequencing System.

TruSight One Sequencing Panel Sample Prep Experienced User Card

Intended for the experienced user, this document summarizes the steps for preparing samples using the TruSight One Sequencing Panel Sample Prep protocol.

Small RNA v1.5 Sample Prep Guide (15002615)

Instructions for using the Small RNA v1.5 sample prep.

MiSeqDx Instrument Package Insert for Instruments with Dual Boot Configuration

For customers that have a MiSeqDx instrument with dual boot upgrade. If you are not sure if your instrument has the dual boot upgrade, contact Illumina Technical Support. This document includes information about the intended use, instructions for use, and performance characteristics of the MiSeqDx Instrument.

TruSeq Small RNA Library Prep Kit Consumables & Equipment

Consumables and equipment used with the TruSeq Small RNA Library Prep Kit. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window.

GenomeStudio DNA Sequencing Module v1.0 User Guide (11319092)

Instructions for using the GenomeStudio DNA Sequencing Module to visualize and analyze sequencing data.

MiSeq Enhancements Customer Letter

This customer letter describes enhancements and components associated with the MiSeq upgrade, and how upgrades are schedule.

Local Run Manager TruSight Tumor 15 Analysis Module Workflow Guide

This guide provides instructions for setting up a run and viewing analysis results using the TruSight Tumor 15 analysis module.

ScriptSeq Complete Gold (Blood) Library Prep Guide

This guide provides instructions for preparing sequencing libraries using the ScriptSeq Complete Gold (Blood) Kit.

TruSeq DNA Sample Preparation (v1) High Throughput Experienced User Card

Instructions for using TruSeq DNA sample prep HT protocol.

MiSeqDx Cystic Fibrosis 139-Variant Assay Package Insert

This document includes information about the intended use, instructions for use, and performance characteristics of the MiSeqDx Cystic Fibrosis 139-Variant Assay.

TruSeq Amplicon - Cancer Panel Library Preparation Guide

Instructions for preparing samples using the TruSeq Amplicon - Cancer Panel Library Preparation Kit.

BaseSpace Core App Guides

Instructions for using the BaseSpace Core Apps: 

  • 16S Metagenomics
  • Amplicon DS
  • BWA Enrichment
  • BWA Whole Genome Sequencing
  • Isaac Enrichment
  • Isaac Whole Genome Sequencing
  • MethylSeq
  • RNA Express
  • Small RNA
  • TopHat and Cufflinks RNA-seq
  • TruSeq Amplicon
  • TruSeq Long-Reads Assembly
  • TruSeq Phasing
  • TruSeq Targeted RNA
  • TruSight Tumor 15
  • Tumor Normal
ScriptSeq Complete (Plant Leaf) Low-Input Library Prep Guide

This guide provides instructions for preparing sequencing libraries using the ScriptSeq Complete (Plant Leaf) Low-Input Kit.

Nextera Rapid Capture Enrichment Sequencing Product Insert

This document outlines the sequencing workflows and requirements with the Nextera Rapid Capture Exome, Expanded Exome, and Custom Enrichment Kits.

TruSeq Amplicon BaseSpace App Documentation

For instructions on using the TruSeq Amplicon BaseSpace App, see either the TruSeq Amplicon 2.0 Online Help or the TruSeq Amplicon 3.0 Online Help.

TruSeq SBS Kit v5 Reagent Preparation Guide (for the Genome Analyzer) (15013595)

Instructions for preparing TruSeq SBS v5 reagents for the Genome Analyzer.

Nextera Mate Pair Gel-Plus Experienced User Card

Intended for the experienced user, this document summarizes the steps for preparing samples using the Nextera Mate Pair Gel-Plus protocol.

MiSeqDx Instrument Package Insert for MOS v2

This document includes information about the intended use, instructions for use, and performance characteristics of the MiSeqDx Instrument. Package insert is for use with the MiSeq Operating Software (MOS) v2. 

ScriptSeq Complete Gold (Human/Mouse/Rat) Library Prep Guide

This guide provides instructions for preparing sequencing libraries using the ScriptSeq Complete Gold (Human/Mouse/Rat) Kit.

VariantStudio Release Notes

Summary of changes introduced in VariantStudio software.

HiSeq System Custom Primers Guide

This guide contains instructions for using custom primers for a sequencing run on the HiSeq 2500, HiSeq 1500, HiSeq 2000, HiSeq 3000, or HiSeq 4000 system.

BlueFuse Multi Software Guide

Instructions for using BlueFuse Multi Software, with chapters about Getting Started, the CytoChip Module, and the Karyomapping Module.

HiSeq 1000 System User Guide (15023355)

Instructions for using the HiSeq 1000 system for sequencing.

Local Run Manager Generate FASTQ Analysis Module Workflow Guide

This guide provides instructions for setting up a run and viewing analysis results using the Generate FASTQ analysis module.

Read 1 Primer Rehyb on a TruSeq v3 Flow Cell

Instructions for performing Read 1 primer rehybridization on a TruSeq v3 (HiSeq) flow cell using the TruSeq v2 cBot Multi-Primer Re-Hybridization Kit.

AmpliSeq for Illumina BRCA Panel Reference Guide

This guide contains everything a first-time user needs, including an overview of the AmpliSeq for Illumina BRCA Panel protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

iSeq 100 Sequencing System Guide

The system guide provides a system overview and instructions for operating and maintaining the iSeq 100 Sequencing System.

TruSeq Amplicon - Cancer Panel Library Preparation Experienced User Card

Experienced-level instructions for preparing samples using the TruSeq Amplicon - Cancer Panel Library Preparation Kit.

Nextera DNA Flex Library Prep Reference Guide
This checklist is a condensed form of the Nextera Flex for Enrichment protocol. It is easy to print and carry with you in the lab.
TruSeq Library Prep Pooling Guide

Guidelines for pooling TruSeq libraries for Illumina sequencing systems that require balanced index combinations.

BaseSpace Software Help

 

For instructions on using BaseSpace, visit help.basespace.illumina.com.

 

BlueFuse Multi Installation Guide

This guide describes how to install BlueFuse Multi for the first time or to upgrade BlueFuse Multi from an earlier release.

Local Run Manager Small RNA Analysis Module Workflow Guide

This guide provides instructions for setting up a run and viewing analysis results using the Small RNA analysis module.

IEM TruSight Tumor 15 Quick Reference Card

Instructions for using IEM with the TruSight Tumor 15 Kit.

AmpliSeq for Illumina Comprehensive Panel v3 Checklist

This checklist is a condensed form of the AmpliSeq for Illumina Comprehensive Panel v3 protocol. It is easy to print and carry with you in the lab.

Nextera XT Sample Preparation Lab Tracking Form

Interactive form for recording sample preparation steps using the Nextera XT sample prep Kit.

MiSeqDx Universal Kit 1.0 Reference Guide

This guide contains best practices and instructions for preparing libraries using the MiSeqDx Universal Kit 1.0.

The European Authorized Representative (EC REP) has changed from Emergo Europe to the following.

Illumina Cambridge Limited
Chesterford Research Park, Little Chesterford
Saffron Walden, CB10 1XL
UNITED KINGDOM

NextSeq 550Dx Instrument Package Insert (IVD)

Instructions for customers in the United States using the NextSeq 550Dx instrument.

MiSeq System Guide

This guide includes information about instrument components, MiSeq Control Software (MCS), and required consumables, and instructions for performing a sequencing run and maintaining the instrument. 

MiSeq System Guide for MiSeq Reporter

This guide includes information about instrument components, MiSeq Control Software (MCS), and required consumables, and instructions for performing a sequencing run and maintaining the instrument. 

NextSeq 550Dx Instrument Reference Guide

Instructions for using the NextSeq 550Dx instrument.

TruSight Tumor 15 Protocol Guide

This guide contains just the steps for the TruSight Tumor 15 protocol. It is intended for users who are experienced with Illumina library prep methods.

NextSeq 500 Kit v2 Documentation

For information about the NextSeq 500 Kit v2, see Contents & Storage and Requirements & Compatibility. For preparation instructions, see the NextSeq 500 System Guide.

Preparing Samples for ChIP Sequencing of DNA

Instructions for preparing samples using the ChIP-Seq sample prep Kit.

ScriptSeq Complete Gold (Human/Mouse/Rat) Low-Input Library Prep Guide

This guide provides instructions for preparing sequencing libraries using the ScriptSeq Complete Gold (Human/Mouse/Rat) Low-Input Kit.

TruSight Tumor 26 Checklist

This checklist is a condensed form of the TruSight Tumor 26 protocol. It is easy to print and carry with you in the lab.

AmpliSeq for Illumina Custom and Community Panels Consumables & Equipment

Consumables and equipment used with the AmpliSeq for Illumina Custom and Community Panels. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window.

TruSeq DNA Dual Index Product Insert

Summary of instructions for using the TruSeq DNA Dual Index.

BWA Enrichment BaseSpace App Documentation

For instructions on using the BWA Enrichment BaseSpace App, see the BWA Enrichment v2.1 Online Help.

TG VeriSeq NIPT Solution Checklist
This checklist is a condensed form of the TG VeriSeq NIPT Solution protocol. It is easy to print and carry with you in the lab.
TruSeq Stranded mRNA Sample Prep Guide

Instructions for using the TruSeq Stranded mRNA sample prep protocol.

TruSeq Stranded mRNA is also offered in the following configuration. Refer to TruSeq Stranded mRNA if you have ordered product 20020594 or 20020595.

HiSeq X Ten Reagent Kit v2 Reference Guide

For information about the HiSeq X Ten Reagent Kit v2, see Contents & Storage. For reagent preparation instructions, see the cBot System Guide and the HiSeq X System Guide.

TruSeq DNA PCR-Free Library Prep Reference Guide

This guide contains everything a first-time user needs, including an overview of the TruSeq DNA PCR-Free Library Prep protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

MiSeq Reagent Kit v3-PGS Reagent Preparation Guide

The MiSeq Reagent Kit v3-PGS Reagent Preparation Guide provides an overview of kit contents and instructions for preparing the reagent cartridge for a sequencing run on the MiSeq for the VeriSeq PGS workflow.

Illumina FFPE QC Kit for TruSeq Amplicon - Cancer Panel and TruSeq Custom Amplicon v1.5

Instructions for using the FFPE QC kit with the TruSeq Amplicon - Cancer Panel Kit or the TruSeq Custom Amplicon Kit.

ForenSeq DNA Signature Prep Checklist

This checklist is a condensed form of the ForenSeq DNA Signature Prep protocol. It is easy to print and carry with you in the lab.

NeoPrep Library Prep System Guide

This guide contains an overview of instrument components and instructions for operating and maintaining the NeoPrep Library Prep System.

MiniSeq System Denature and Dilute Libraries Guide

This guide contains instructions for denaturing and diluting libraries before sequencing on the MiniSeq System, and instructions for preparing a PhiX control.

TruSight HLA v2 Sequencing Panel Reference Guide

This guide contains everything a first-time user needs, including an overview of the TruSight HLA v2 Sequencing Panel protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

GenomeStudio ChIP Sequencing Module v1.0 User Guide (11319084)

Instructions for using the GenomeStudio ChIP Sequencing Module.

IEM Nextera Quick Reference Card

Instructions for using IEM with the Nextera library prep kits.

HiSeq Analysis Software v2.1 Release Notes

HiSeq Analysis Software v2.1 release notes describe features and changes introduced in the latest versions of the HiSeq Analysis Software v2.1.

Cluster Station Support - Decontamination Procedure Download

This download contains instructions on how to prepare a Cluster Station for shipping.

BaseSpace Onsite Sequence Hub Release Notes

Release Notes for BaseSpace Onsite

AmpliSeq for Illumina Myeloid Panel Consumables & Equipment

Consumables and equipment used with the AmpliSeq for Illumina Myeloid Panel. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window.

TruSeq Synthetic Long-Read DNA Library Prep Guide

Instructions for preparing libraries using the TruSeq Synthetic Long-Read DNA Library Prep and TruSeq Synthetic Long-Read DNA Barcode kits.

TruSeq Nano DNA Library Prep User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq Nano DNA Library Prep Reference Guide.

ScriptSeq Complete Gold (Yeast) Library Prep Guide

This guide provides instructions for preparing sequencing libraries using the ScriptSeq Complete Gold (Yeast) Kit.

MiSeqDx Cystic Fibrosis Clinical Sequencing Assay Package Insert

This document includes information about the intended use, instructions for use, and performance characteristics of the MiSeqDx Cystic Fibrosis Clinical Sequencing Assay.

Nextera DNA Sample Preparation Guide

Instructions for preparing samples using the Nextera DNA sample preparation Kit.

Small RNA Sample Prep Guide (1004239)

Instructions for performing the Small RNA sample prep assay.

MiSeq FGx Forensic Genomics System Software Release Notes

 

MiSeq FGx Forensic Genomics System software release notes describe features and changes introduced in the latest versions of MiSeq FGx Control Software and related software components, including ForenSeq Universal Analysis Software.

 

16S Metagenomics BaseSpace App Documentation

For instructions on using the 16S Metagenomics BaseSpace App, see 16S Metagenomics v1.0 Online Help.

cBot 2 System Safety and Compliance Guide

The safety and compliance guide contains safety considerations and product compliance markings for the cBot 2 system.

NextSeq 550Dx Instrument Safety and Compliance Guide

Safety information and product compliance statements for the NextSeq 550Dx instrument.

HiSeq 2500 System Guide

This guide provides an overview of instrument components and instructions for operating and maintaining the HiSeq 2500. Workflows include HiSeq v4, TruSeq v3, and Rapid Run.

TruSeq Targeted RNA Expression User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq Targeted RNA Expression Guide.

CASAVA v1.8 Changes

Summary of changes introduced in CASAVA v1.8.

MiSeq FGx Reagent Kit Reference Guide

 

Reagent prep guide contain an overview of kit contents and instructions for preparing the reagent cartridge for a sequencing run on the MiSeq FGx.

 

Sequencing Analysis Viewer Software Guide

This guide includes instructions for installing and using Sequencing Analysis Viewer (SAV) software to view metrics generated by the real-time analysis software on Illumina sequencing systems.

AmpliSeq for Illumina Myeloid Panel Checklist

This checklist is a condensed form of the AmpliSeq for Illumina Myeloid Panel protocol. It is easy to print and carry with you in the lab.

TruSeq Ribo Profile Bioinformatics User Guide

This guide provides information about the TruSeq Ribo Profile analysis pipeline.

ForenSeq DNA Signature Prep Reference Guide

This guide contains everything a first-time user needs, including an overview of the ForenSeq DNA Signature Prep protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

Local Run Manager Germline Variant Analysis Module Workflow Guide for MiSeqDx

Instructions for setting up a run and viewing analysis results using the Germline Variant analysis module for the MiSeqDx.

AmpliSeq for Illumina Immune Repertoire Panel Checklist

This checklist is a condensed form of the AmpliSeq for Illumina Immune Repertoire Panel protocol. It is easy to print and carry with you in the lab.

MiniSeq System Safety and Compliance Guides

The safety and compliance guide contains safety considerations and product compliance markings for the MiniSeq System.

The RFID Reader guide contains compliance information for the RFID reader module, an internal component of the MiniSeq System.

MiSeqDx Universal Kit 1.0 Lab Tracking Form

This document summarizes the steps in the MiSeqDx Universal Kit 1.0 and includes fields for recording reagent lot numbers, as well as start and stop times for various steps.

The European Authorized Representative (EC REP) has changed from Emergo Europe to the following.

Illumina Cambridge Limited
Chesterford Research Park, Little Chesterford
Saffron Walden, CB10 1XL
UNITED KINGDOM

AmpliSeq for Illumina Focus Panel Checklist

This checklist is a condensed form of the AmpliSeq for Illumina Focus Panel protocol. It is easy to print and carry with you in the lab.

HiSeq 1500 and HiSeq 2000 Systems Safety and Compliance Guide

The safety and compliance guide describes safety considerations and lists product compliance markings for the HiSeq 1500 and HiSeq 2500 systems.

VeriSeq PGS Library Preparation Experienced User Card and Lab Tracking Form
Experienced-level instructions for preparing samples using the VeriSeq PGS Library Preparation Kit.
MiSeqDx Cystic Fibrosis 139-Variant Assay Lab Tracking Form

This document summarizes the steps in the MiSeqDx Cystic Fibrosis 139-Variant Assay and includes fields for recording reagent lot numbers, as well as start and stop times for various steps.

TruSeq Custom Amplicon Low Input Kit Checklist

This checklist is a condensed form of the TruSeq Custom Amplicon Low Input Kit protocol. It is easy to print and carry with you in the lab.

IEM NeoPrep Quick Reference Card

Instructions for using IEM with the NeoPrep Library Prep System.

Trim Adapters for Nextera DNA Flex Kits in MiniSeq LRM

This quick reference card describes how to set the adapter trimming sequences for the Nextera DNA Flex library prep kit specifically on sequencing runs using an Illumina MiniSeq.

TruSight HLA Sequencing Panel Protocol Guide

This guide contains just the steps needed to prepare TruSight HLA libraries. It is intended for users who are experienced with Illumina library prep methods.

Nextera XT DNA Library Prep Kit Checklist

This checklist is a condensed form of the Nextera XT DNA protocol. It is easy to print and carry with you in the lab.

HiSeq v4 System Upgrade Welcome Letter

This letter was sent to customers about their HiSeq v4 system upgrade.

AmpliSeq for Illumina Comprehensive Panel v3 Reference Guide

This guide contains everything a first-time user needs, including an overview of the AmpliSeq for Illumina Comprehensive Panel v3 protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

TruSeq Small RNA Library Prep Kit Reference Guide

This guide contains everything a first-time user needs, including an overview of the TruSeq Small RNA protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

cBot Safety and Compliance Guide

The safety and compliance booklet contains safety considerations and product compliance markings for the cBot system.

ScriptSeq v2 RNA-Seq Library Prep Guide

This guide provides instructions for preparing sequencing libraries using the ScriptSeq v2 RNA-Seq Library Prep Kit.

FastTrack Phasing Analysis Services Guide

This document provides an overview of the FastTrack Phasing Informatics Pipeline 1.1.0. deliverables and phasing algorithm. FastTrack Phasing Informatics Pipeline uses Prism v2.2, the same algorithm used in the TruSeq Phasing Analysis BaseSpace App. The purpose of this document is to help you understand the Phasing Analysis Service data package you receive from Illumina.

TruSeq Custom Amplicon Library Preparation Experienced User Card and Lab Tracking Form

Experienced user level instructions for preparing samples using the TruSeq Custom Amplicon Library Preparation Kit.

Nextera DNA Flex Library Prep Reference Guide

This guide contains everything a first-time user needs, including an overview of the Nextera Flex for Enrichment protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

TruSeq Synthetic Long-Read DNA Library Prep Experienced User Card and Lab Tracking Form

Experienced-level instructions for preparing libraries using the TruSeq Synthetic Long-Read DNA Library Prep and TruSeq Synthetic Long-Read DNA Barcode kits.

TruSight Rapid Capture Sample Prep Guide

Instructions for using the TruSight Rapid Capture Sample Prep Kit to prepare up to 96 indexed paired-end libraries, followed by enrichment using the TruSight Content Set CSO (custom selected oligos).

TruSeq Amplicon - Cancer Panel Lab Tracking Form

Interactive form for recording sample preparation steps using the TruSeq Amplicon - Cancer Panel kit.

AmpliSeq for Illumina Custom and Community Panels DNA Checklist

This checklist is a condensed form of the AmpliSeq for Illumina Custom and Community Panels DNA protocol. It is easy to print and carry with you in the lab.

TruSight RNA Pan-Cancer Panel Reference Guide

This guide contains everything a first-time user needs, including an overview of the TruSight RNA Pan-Cancer Panel protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

MiSeq Reporter Analysis Workflow Reference Guides

Each workflow reference guide contains an overview of the analysis workflow and descriptions of analysis output files. For information about the MiSeq Reporter interface and instructions for instructions for installing, using, and troubleshooting the software, see the MiSeq Reporter User Guide.

Local Run Manager Resequencing Analysis Module Workflow Guide

This guide provides instructions for setting up a run and viewing analysis results using the Resequencing analysis module.

HiScanSQ System User Guide (15015392)

Instructions for using the HiScanSQ.

Multiplexing Sample Prep Guide (1005361)

Instructions for performing the Multiplexing sample prep assay.

Local Run Manager Resequencing Analysis Module Workflow Guide

This guide provides instructions for setting up a run and viewing analysis results using the Resequencing analysis module.

TruSeq RNA Sample Prep v2 Guide

Instructions for preparing samples using the TruSeq RNA Sample Preparation Kit v2.

TruSeq Stranded Total RNA Sample Preparation LS EUC and LTF

Experienced-level instructions for preparing samples using the LS protocol for the TruSeq Stranded Total RNA Sample Prep Kit.

GenomeStudio 2008.1 Framework UG (11318815)

Overview of the GenomeStudio interface used by all GenomeStudio software modules.

HiSeq Analysis Software User Guide

HiSeq Analysis Software User Guide

MiSeq Run Workflow Quick Reference Cards

Each quick reference card provides a graphical representation of the MiSeq analysis workflow for the experienced user. Workflows include Assembly, Enrichment, Library QC, Metagenomics, PCR Amplicon, Resequencing, Small RNA, and TruSeq Amplicon.

TruSight RNA Pan-Cancer Panel Protocol Guide

This guide contains just the steps for the TruSight RNA Pan-Cancer Panel protocol. It is intended for users who are experienced with Illumina library prep methods.

ForenSeq Universal Analysis Software Guide

This guide provides an overview of the ForenSeq Universal Analysis Software interface and instructions for use. 

MiSeq Reporter Amplicon - DS Workflow Reference Guide

This guide provides an overview of the MiSeq Reporter Amplicon - DS analysis workflow, including installation instructions, workflow requirements, and descriptions of analysis output files.

BaseSpace Variant Interpreter Release Notes

Summary of changes introduced in BaseSpace Variant Interpreter software.

Nextera Rapid Capture Enrichment Reference Guide

This guide contains everything a first-time user needs, including an overview of the Nextera Rapid Capture Enrichment protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

TruSeq DNA PCR-Free Library Prep User-Supplied Consumables and Equipment

 

Consumables and equipment excerpt from the TruSeq DNA PCR-Free Library Prep Reference Guide.

 

Local Run Manager RNA Fusion Analysis Module Workflow Guide

This guide provides instructions for setting up a run and viewing analysis results using the RNA Fusion analysis module.

Nextera DNA Flex Dried Blood Spot Protocol Guide

Instructions for preparing samples from Dried Blood Spot cards.

TruSeq Cluster Kit v5 (CS-GA) Reagent Prep Guide

This guide contains descriptions of kit components and reagent preparation instructions for the Cluster Station.

AmpliSeq for Illumina Comprehensive Panel v3 Consumables & Equipment

Consumables and equipment used with the AmpliSeq for Illumina Comprehensive Panel v3. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window.

AmpliSeq for Illumina Custom and Community Panels Reference Guide

This guide contains everything a first-time user needs, including an overview of the AmpliSeq for Illumina Custom and Community Panels protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

TruSeq HT Dual Index Quick Reference Card

This document outlines dual index sequencing workflows and requirements for the TruSeq Nano DNA HT Sample Prep Kit.

TruSeq Nano DNA Library Prep for NeoPrep Reference Guide

This guide contains everything a first-time user needs, including an overview of the TruSeq Nano DNA Library Prep for NeoPrep protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

BaseSpace Onsite LT System Guide

This guide contains instructions for using the BaseSpace Onsite LT System, a genomics analysis platform that is a directly integrated end-to-end solution for the MiSeq System.

TruSeq Sample Prep Best Practices Guide

Overview of the best practices for the TruSeq sample prep protocol.

MiSeq System Denature and Dilute Libraries Guide

This guide provides instructions for denaturing and diluting libraries after llibrary preparation and before sequencing on the MiSeq. This guide also includes instructions for preparing a PhiX control.

HiSeq X System Safety and Compliance Guide

The safety and compliance guide describes safety considerations and lists product compliance markings for the HiSeq X system.

cBot System Guide

This guide contains instructions for using the cBot for cluster generation on flow cells for the HiSeq X, HiSeq 4000, HiSeq 3000, HiSeq high output runs, HiSeq rapid runs, and Genome Analyzer.

AmpliSeq for Illumina Immune Response Panel Reference Guide

This guide contains everything a first-time user needs, including an overview of the AmpliSeq for Illumina Immune Response Panel protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

Nextera DNA Flex Library Prep Consumables & Equipment

Consumables and equipment used with the Nextera DNA Flex Kit. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window.

IEM TruSeq Small RNA Quick Reference Card

Instructions for using IEM with the TruSeq Small RNA Sample Prep Kit.

Preparing Samples for Analysis of Small RNA Using the Oligo Only Kit (1003651)

Instructions for preparing samples using the Small RNA Oligo Only Kit.

TruSeq ChIP Sample Prep Guide

Instructions for using the TruSeq ChIP Sample Prep Kit to prepare samples for sequencing.

mtDNA Variant Analyzer BaseSpace App Documentation

For instructions on using the mtDNA Variant Analyzer BaseSpace App, see mtDNA Variant Analyzer v1.0 Online Help.

NextSeq 500 Quick Reference Cards

 

These application workflow cards provide guidance for planning, running, and analyzing a NextSeq 500 project.

Languages: Chinese, Korean, German, Spanish, French, and Italian.

 

Cufflinks Assembly & DE BaseSpace App Documentation

For instructions on using the Cufflinks Assembly & DE BaseSpace App, see Cufflinks Assembly & DE v1.0 Online Help.

TruSeq Stranded mRNA Library Prep for NeoPrep Protocol Guide

This guide contains just the steps needed to prepare TruSeq Stranded mRNA-NeoPrep libraries. It is intended for users who are experienced with NeoPrep library prep methods.

TruSeq DNA Sample Preparation (v1) Low Throughput Lab Tracking Form

Lab tracking form for the TruSeq DNA sample prep protocol.

HiSeq X System Guide

The system user guide describes instrument components, on-instrument software, the sequencing workflow, and maintenance procedures.

TG VeriSeq NIPT Solution Reference Guide
This guide contains everything a first-time user needs, including an overview of the TG VeriSeq NIPT Solution protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.
Small RNA BaseSpace App Documentation

For instructions on using the Small RNA BaseSpace App, see Small RNA v1.0 App Online Help.

ScriptSeq Complete (Plant Leaf) Library Prep Guide

This guide provides instructions for preparing sequencing libraries using the ScriptSeq Complete (Plant Leaf) Kit.

TruSeq Nano DNA Library Prep for NeoPrep Protocol Guide

This guide contains just the steps needed to prepare TruSeq Nano DNA-NeoPrep libraries. It is intended for users who are experienced with NeoPrep library prep methods.

Nextera DNA Flex Library Prep Reference Guide

This guide contains everything a first-time user needs, including an overview of the Nextera DNA Flex protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

Nextera DNA Sample Preparation Product Insert

This download contains the product insert listing the necessary sample preparation kits, software, and documentation for Nextera DNA Sample Preparation as well as pooling guidelines and requirements for enabling dual indexing.

MiSeqDx Instrument Safety and Compliance Guide

This guide contains safety information and product compliance markings for the MiSeqDx instrument.

Sequencing TruSight HLA v2 Libraries on a MiniSeq System Quick Reference Guide

This quick reference guide contains the procedure for sequencing TruSight HLA v2 libraries on a MiniSeq System.

TruSeq DNA PCR-Free Library Prep Protocol Guide

This guide contains just the steps needed to prepare TruSeq DNA PCR-Free libraries. It is intended for users who are experienced with Illumina library prep methods.

BaseSpace Onsite v2.0 User Guide

This guide contains instructions for using the BaseSpace Onsite System, a genomics analysis platform that is a directly integrated end-to-end solution.

AmpliSeq for Illumina Cancer HotSpot Panel v2 Consumables & Equipment

Consumables and equipment used with the AmpliSeq for Illumina Cancer HotSpot Panel v2. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window.

Paired-End Sample Preparation User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the Paired-End Sample Preparation Guide.

BaseSpace Onsite Software Upgrade Guide

This document explains how to update your BaseSpace Onsite Software through the Admin Panel Updates page.

For a BaseSpace Onsite v2.1 upgrade kit, contact techsupport@illumina.com.

HiSeq 2000 System Guide

This guide provides an overview of instrument components and instructions for operating and maintaining the HiSeq 2000.

Sequencing Library qPCR Quantification Guide

This download contains the protocol guide for SBS library qPCR quantification.

TruSeq RNA Access Library Prep User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq RNA Access Library Prep Guide, 15049525 A

MiSeq Reagent Kit Reagent Preparation Guide

MiSeq Reagent Kit Reagent Prep Guides provide an overview of kit contents and instructions for preparing the reagent cartridge for a sequencing run on the MiSeq.

TruSeq Stranded mRNA Sample Prep LS EUC and LTF

Experienced-level instructions for preparing samples using the LS protocol for the TruSeq Stranded mRNA Sample Prep Kit.

HiSeq X Five Reagent Kit v2 Reference Guide

For information about the HiSeq X Five Reagent Kit v2, see Contents & Storage. For reagent preparation instructions, see the cBot System Guide and the HiSeq X System Guide.

Nextera Enrichment Sample Preparation Lab Tracking Form

Interactive form for recording sample preparation steps using the Nextera Enrichment sample prep Kit.

NextSeq 550Dx High Output Reagent Kit v2 (300 Cycles)

Instructions for using the NextSeq 550Dx High Output Reagent Kit v2 (300 Cycles).

MiSeq Reporter Software Reference Guide for IVD Assays

This guide describes the MiSeq Reporter user interface, defines concepts and terms, and explains the folders, files, and data generated from the Amplicon workflow used to analyze MiSeqDx Cystic Fibrosis Assays.

Sequencing Dual-Indexed Libraries on the HiSeq

This guide contains instructions for sequencing dual-indexed libraries on the HiSeq.

MiSeq FGx Instrument Site Prep Guide

 

This guide provides requirements for preparing your lab for a MiSeq FGx Forensic Genomics System: lab space requirements, electrical requirements, bench recommendations, UPS recommendations, and user-supplied consumables.

 

Illumina Experiment Manager User Guide

Instructions for using the Illumina Experiment Manager.

Running TruSight Tumor 26 Analysis on HiSeq 2500

This guide includes instructions for generating, sequencing, and analyzing TruSight Tumor 26 libraries with the HiSeq 2500.

VariantStudio User Guide

This guide provides an overview of the Illumina VariantStudio desktop application and instructions for importing, annotating, and filtering variants.

TruSight HLA v2 Sequencing Panel Checklist

This checklist is a condensed form of the TruSight HLA v2 Sequencing Panel protocol. It is easy to print and carry with you in the lab.

AmpliSeq for Illumina Transcriptome Human Gene Expression Panel Consumables & Equipment

Consumables and equipment used with the AmpliSeq for Illumina Transcriptome Human Gene Expression Panel. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window.

HiScanSQ System Sequencing Best Practices (15029252)

Best practices poster for the HiScanSQ system.

MiSeqDx Universal Kit 1.0 Package Insert

This document includes information about the intended use, instructions for use, and performance characteristics of the MiSeqDx Universal Kit.

The European Authorized Representative (EC REP) has changed from Emergo Europe to the following.

Illumina Cambridge Limited
Chesterford Research Park, Little Chesterford
Saffron Walden, CB10 1XL
UNITED KINGDOM

AmpliSeq for Illumina BRCA Panel Checklist

This checklist is a condensed form of the AmpliSeq for Illumina BRCA Panel protocol. It is easy to print and carry with you in the lab.

User-supplied consumables and equipment excerpt from the TruSeq RNA Sample Preparation v2 Guide.

Consumables and equipment excerpt from the TruSeq RNA Sample Preparation v2 Guide.

ScriptSeq Complete Gold (Epidemiology) Low-Input Library Prep Guide

This guide provides instructions for preparing sequencing libraries using the ScriptSeq Complete Gold (Epidemiology) Low-Input Kit.

BaseSpace Sequence Hub Enterprise Domain Admin Quick Reference Card

Instructions for the BaseSpace Sequence Hub Enterprise Domain Administrator.

TruSeq Small RNA Library Prep Kit Checklist

This checklist is a condensed form of the TruSeq Small RNA protocol. It is easy to print and carry with you in the lab.

BlueFuse Workflow Manager User Guide (1000000028842)

Instructions for using the BlueFuse Workflow Manager with VeriSeq PGS.

Genome Analyzer IIx (SCS v2.10) Quick Reference Guide (15030967)

This guide contains instructions for the experienced user for sequencing on the Genome Analyzer.

Local Run Manager RNA Fusion Analysis Module Workflow Guide

This guide provides instructions for setting up a run and viewing analysis results using the RNA Fusion analysis module.

Preparing Samples for Sequencing Genomic DNA (1003806)

Instructions for preparing samples using the Genomic DNA kit.

HiSeq Safety and Compliance Guide

This guide contains safety information and product compliance statements for the HiSeq.

TruSeq Rapid Cluster Kit Reagent Prep Guide

For information about the TruSeq Rapid Cluster Kit, see Contents & Storage and Requirements & Compatibility. For preparation instructions, see the cBot System Guide.

TruSeq Amplicon - Cancer Panel Resources (15033227)

Links to documentation, accessories, and product files for the TruSeq Amplicon - Cancel Panel.

Sequencing Kit v4 Reagent Preparation Guide (15002739)

Instructions for using the Reagent Preparation for the Genome Analyzer - Sequencing Kit v4

CASAVA 1.8.2 Quick Reference Guide (15011197)

Reference Guide for CASAVA v1.8.2 software.

BaseSpace Onsite HT System Guide

This guide contains instructions for using the BaseSpace Onsite HT System, a genomics analysis platform that is a directly integrated end-to-end solution for the MiSeq, NextSeq 500, NextSeq 550, NeoPrep, HiSeq 1000, HiSeq 1500. HiSeq 2000, HiSeq 2500, HiSeq 3000, HiSeq 4000 Systems.

mtDNA Variant Processor BaseSpace App Documentation

For instructions on using the mtDNA Variant Processor BaseSpace App, see mtDNA Variant Processor v1.0 Online Help.

Fungal Metagenomic Sequencing Demonstrated Protocol
The Fungal Metagenomic Sequencing Demonstrated Protocol is for the analysis of fungal or metagenomic samples, and describes primer sequences and an assay workflow for use with a BaseSpace Sequence Hub analysis solution.
MiSeq Reporter Software Guide (15042295)

This guide provides an overview of the MiSeq Reporter interface and instructions for using the MiSeq Reporter. For information about analysis workflows, see the MiSeq Reporter Workflow Reference Guides.

Globin-Zero Gold rRNA Removal Kit Reference Guide

This guide provides instructions for removing rRNA and globin mRNA from samples.

TruSeq DNA Methylation Kit Reference Guide

This guide provides instructions for preparing libraries using the TruSeq DNA Methylation Kit.

ScriptSeq Index PCR Primers Guide

This guide provides instructions for preparing sequencing libraries using the ScriptSeq Index PCR Primers Kit.

Using the Paired-End Cluster Generation Kit v2 on the Cluster Station and Paired-End Module (1005629)

Instructions for using the Paired-End Cluster Generation Kit v2 on the Cluster Station and Paired-End Module.

HiSeq SBS Kit v4 Reference Guide

For information about the HiSeq SBS Kit v4, see Contents & Storage and Requirements & Compatibility. For preparation instructions, see the HiSeq 2500 System GuideHiSeq 1500 System Guide, or HiSeq 2000 System Guide.

TruSeq DNA Sample Preparation (v1) Low Throughput Experienced User Card

Instructions for using the TruSeq DNA sample prep LT protocol.

TruSeq Stranded mRNA Sample Preparation User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq Stranded mRNA Sample Preparation Guide.

MiSeqDx Library Prep Check Kit Quick Reference Card

This document includes information regarding the use of the MiSeqDx Library Prep Check Kit.

TruSight Cardio Sequencing Panel Protocol Guide

This guide contains just the steps needed to prepare TruSight Cardio libraries. It is intended for users who are experienced with Illumina library prep methods.

TruSight Cardio Sequencing Panel Checklist

This checklist is a condensed form of the TruSight Cardio protocol. It is easy to print and carry with you in the lab.

NeoPrep System Safety and Compliance Guide

This safety and compliance guide contains safety considerations and product compliance markings for the NeoPrep Library Prep System.

TruSeq RNA Sample Preparation High Throughput Experienced User Card

Instructions for using the TruSeq RNA sample prep HT protocol.

TruSeq Nano DNA Library Prep Reference Guide

This guide contains everything a first-time user needs, including an overview of the TruSeq Nano DNA Library Prep protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

AmpliSeq for Illumina Custom and Community Panels RNA Checklist

This checklist is a condensed form of the AmpliSeq for Illumina Custom and Community Panels RNA protocol. It is easy to print and carry with you in the lab.

HiSeq X Software v3.1.26 Release Notes

This document describes the changes and features introduced in HiSeq X software package v3.1.26, which includes HiSeq X Control Software v3.1.26 and updates to RTA, recipes, the BaseSpace Broker, and Sequencing Analysis Viewer software.

HiSeq 2500, 1500, and 2000 Systems Site Prep Guide

This guide provides lab specifications and requirements for preparing the lab for sequencing on the HiSeq 2500, HiSeq 1500, or HiSeq 2000 system.

NextSeq 550Dx Symbol Key

Explanations of symbols used in labeling for NextSeq 550Dx.

Local Run Manager Small RNA Analysis Module Workflow Guide

This guide provides instructions for setting up a run and viewing analysis results using the Small RNA analysis module.

VeriSeq NIPT Workflow Manager Guide

Instructions for using Workflow Manager software

AmpliSeq for Illumina Exome Panel Consumables & Equipment

This checklist is a condensed form of the AmpliSeq for Illumina Exome Panel protocol. It is easy to print and carry with you in the lab.

Amplicon DS BaseSpace App Documentation

For instructions on using the Amplicon DS BaseSpace App, see Amplicon DS v1.2 Online Help.

NovaSeq Series Custom Primers Guide

This guide provides instructions for using custom primers on the NovaSeq Sequencing System.

Frequently Asked Questions (FAQs) for the Master Lot Sheet (MLS)

Frequently Asked Questions (FAQs) for the Master Lot Sheet (MLS)

TruSeq ChIP Sample Preparation User-Supplied Consumables and Equipment

Consumables and equipment excerpt from the TruSeq ChIP Sample Preparation Guide.

MiSeqDx Instrument Operation Manual for China
For MiSeqDx customers in China. This document includes information about the intended use, performance characteristics, safety considerations, site preparation, instrument components, software, consumables, and instructions for performing a sequencing run and maintaining the MiSeqDx instrument.
Nextera Rapid Capture Enrichment Checklist

This checklist is a condensed form of the Nextera Rapid Capture Enrichment protocol. It is easy to print and carry with you in the lab.

TruSeq Stranded Total RNA Dual Index Product Insert

Instructions for dual-indexing with TruSeq Stranded Total RNA HT Sample Prep.

TruSeq Phasing BaseSpace App Documentation

For instructions on using the TruSeq Phasing BaseSpace App, see TruSeq Phasing v1.1 Online Help.

MiniSeq System Custom Primers Guide

This guide contains instructions for using custom primers on the MiniSeq system.

NeoPrep System Site Prep Guide

This guide contains lab specifications and requirements for operating the NeoPrep Library Prep System.

CASAVA Software Version 1.8 User Guide (15011196 B)

This download contains the user guide for the CASAVA v1.8 sequencing analysis software.

ForenSeq DNA Signature Prep Consumables and Equipment List

Consumables and equipment used with the ForenSeq DNA Signature Prep Kit. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window.

Indexed Sequencing Overview Guide

This guide provides an overview of the indexed sequencing process for single-indexing and dual-indexing workflows on the iSeq, NovaSeq, MiniSeq, NextSeq, MiSeq, and HiSeq sequencing systems.

TruSeq DNA Sample Preparation Guide

Instructions for preparing samples using the TruSeq DNA Sample Prep Kit.

MiSeq System Custom Primers Guide

This guide provides instructions for using custom primers for sequencing on the MiSeq.

MiniSeq System Safety and Compliance Guide

The safety and compliance guide contains safety considerations and product compliance markings for the MiniSeq System.

IEM TruSeq Targeted RNA Expression Quick Reference Card

Instructions for using IEM with the TruSeq Targeted RNA Expression kits.

AmpliSeq for Illumina Myeloid Panel Reference Guide

This guide contains everything a first-time user needs, including an overview of the AmpliSeq for Illumina Myeloid Panel protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

Local Run Manager DNA Enrichment Analysis Module Workflow Guide

This guide provides instructions for setting up a run and viewing analysis results using the DNA Enrichment analysis module.

NextSeq System Denature and Dilute Libraries Guide

This guide contains instructions for denaturing and diluting libraries after library preparation and before sequencing on the NextSeq System. This guide also includes instructions for preparing a PhiX control.

HiSeq 4000 and HiSeq 3000 Systems Site Prep Guide

The site prep guide contains lab specifications and requirements for preparing the lab for sequencing on the HiSeq 4000 or HiSeq 3000 system.

TruSight Tumor 15 Reference Guide

This guide contains everything a first-time user needs, including an overview of the TruSight Tumor 15 protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

ScriptSeq Complete (Human/Mouse/Rat) Library Prep Guide

This guide provides instructions for preparing sequencing libraries using the ScriptSeq Complete (Human/Mouse/Rat) Kit.

MiSeqDx Instrument Package Insert

This document includes information about the intended use, instructions for use, and performance characteristics of the MiSeqDx Instrument. For customers that do not have a MiSeqDx instrument with dual boot upgrade. If you are not sure if your instrument has the dual boot upgrade, contact Illumina Technical Support.

AmpliSeq for Illumina Immune Repertoire Panel Consumables & Equipment

Consumables and equipment used with the AmpliSeq for Illumina Immune Repertoire Panel. Download this form to a preferred location before using it. The interactivity in this form is not designed for use in a browser window.

AmpliSeq for Illumina Focus Panel Reference Guide

This guide contains everything a first-time user needs, including an overview of the AmpliSeq for Illumina Focus Panel protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

BlueFuse Multi Release Notes

Describes new features and updates to the BlueFuse Multi v4.4 Software.

RFID Reader Compliance Guide

The RFID guide provides compliance information for the RFID reader module, an internal component of the iSeq 100 Sequencing System, NovaSeq Sequencing System, and the MiniSeq System.

TruSeq RNA Access Library Prep Experienced User Card and Lab Tracking Form

Experienced-level instructions for preparing libraries using the TruSeq RNA Access Library Prep Kit.

TruSeq DNA Sample Preparation (v1) Guide

Instructions for using the TruSeq DNA sample prep (v1) protocol.

MiSeqDx Cystic Fibrosis 139-Variant Assay Reference Guide

This guide contains best practices and instructions for preparing libraries using the MiSeqDx Cystic Fibrosis 139-Variant Assay.

ScriptSeq Complete (Plant Seed/Root) Low-Input Library Prep Guide

This guide provides instructions for preparing sequencing libraries using the ScriptSeq Complete (Plant Seed/Root) Low-Input Kit.

AmpliSeq for Illumina Immune Response Panel Checklist

This checklist is a condensed form of the AmpliSeq for Illumina Immune Response Panel protocol. It is easy to print and carry with you in the lab.

NextSeq 550Dx Instrument Site Prep Guide

Information about preparing the lab for the NextSeq 550Dx instrument.

TruSight Cardio Sequencing Panel Reference Guide

This guide contains everything a first-time user needs, including an overview of the TruSight Cardio protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

TruSeq Cluster Kit v3 Reagent Prep Guide

For information about the TruSeq Cluster Kit v3, see Contents & Storage and Requirements & Compatibility. For preparation instructions, see the cBot System Guide.

IEM TruSeq Synthetic Long-Read DNA Quick Reference Card

Instructions for using IEM with the TruSeq Synthetic Long-Read DNA Library Prep and TruSeq Synthetic Long-Read DNA Barcode kits.

HiSeq v4 System Upgrade Information Sheet

This document describes key upgrade features, upgrade components, software upgrade features, and new chemistry features for the v4 upgrade.

Primer Rehybridization on a HiSeq Rapid Flow Cell

This guide contains instructions for performing primer rehybridization on the HiSeq using the HiSeq Rapid Rehybridization Kit or the TruSeq Rapid Rehybridization Kit.

BlueFuse Workflow Manager Quick Reference Card

Instructions for using the BlueFuse Workflow Manager to create VeriSeq PGS worklists and sample sheets.

MiSeq System Safety and Compliance Guide

This guide contains safety information and product compliance markings for the MiSeq System.

TruSight Tumor 26 Reference Guide

This guide contains everything a first-time user needs, including an overview of the TruSight Tumor 26 protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

TruSeq Stranded mRNA Library Prep for NeoPrep Reference Guide

This guide contains everything a first-time user needs, including an overview of the TruSeq Stranded mRNA Library Prep for NeoPrep protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

TG VeriSeq NIPT Solution Software Guide
This guide contains instructions for using the TG VeriSeq NIPT Solution Software.
NextSeq 550Dx Instrument Package Insert (CE-IVD)

Instructions for customers in the European Union using the NextSeq 550Dx instrument.  

IEM TruSight HLA Quick Reference Card

Instructions for using IEM with the TruSight HLA Sequencing Panel.

TruSight One Sequencing Panel Reference Guide

This guide contains everything a first-time user needs, including an overview of the TruSight One Sequencing Panel protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

TruSeq Ribo Profile (Yeast) Reference Guide

This guide contains an overview of the TruSeq Ribo Profile (Yeast) protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables and equipment.

ScriptSeq Complete (Bacteria) Low-Input Library Prep Guide

This guide provides instructions for preparing sequencing libraries using the ScriptSeq Complete (Bacteria) Low-Input Kit.

Nextera Enrichment Sample Preparation Experienced User Card

Experienced-level instructions for preparing samples using the Nextera Enrichment Kit.

Nextera XT DNA Library Prep Kit Reference Guide

This guide contains everything a first-time user needs, including an overview of the Nextera XT DNA protocol, tips and techniques, protocol steps, kit contents, and user-supplied consumables.

cBot 2 System Guide

This guide contains instructions for using the cBot 2 system for cluster generation with or without positive sample tracking on a HiSeq X, HiSeq, or Genome Analyzer flow cell.

Whole-Genome Bisulfite Sequencing for Methylation Analysis Guide (15021861)

Instructions for WGBS for Methylation Analysis.

TruSeq RNA Access Library Prep Guide

Instructions for preparing libraries using the TruSeq RNA Access Library Prep Kit.

BaseSpace Core Apps Release Notes

BaseSpace Core Apps software release notes describe features and changes introduced in the latest versions.

Using a PhiX Control for TruSight HLA v2 Sequencing Runs Quick Reference Guide

This quick reference guide contains the procedure for using a PhiX control for TruSight HLA v2 sequencing runs.

Genome Analyzer PE Lab Tracking Form (15014599)

This download contains the interactive lab tracking form for the Genome Analyzer.