Requirements & Compatibility

Requirements & Compatibility

Version Compatibility of Run Components

For best performance and run results, always use compatible versions of SBS reagents and HiSeq Control Software for the flow cell that you are using.

High Output

Cluster Kit Versions SBS Kit Version Software Version
HiSeq Cluster Kit v4 with Flow Cell v4 HiSeq SBS Kit v4 HCS v2.2 or later
TruSeq Cluster Kit v3 with Flow Cell v3 TruSeq SBS Kit v3 HCS v2.0 or later

Rapid Run

Cluster Kit Versions SBS Kit Version Software Version
HiSeq Rapid PE Cluster Kit v2 with Rapid Flow Cell v2
HiSeq Rapid SR Cluster Kit v2 with Rapid Flow Cell v2
HiSeq Rapid Duo cBot Sample Loading Kit
HiSeq Rapid SBS Kit v2 HCS v2.2 or later
TruSeq Rapid PE Cluster Kit with Rapid Flow Cell
TruSeq Rapid SR Cluster Kit with Rapid Flow Cell
TruSeq Rapid Duo cBot Sample Loading Kit
TruSeq Rapid SBS Kit - HS HCS v2.0 or later

Sequencing Primers for Dual-Indexed Libraries

Sequencing primers provided in the TruSeq Dual Index Sequencing Primer Box are required for sequencing the following libraries on the HiSeq when using the TruSeq Cluster Kit v3. If you are using the HiSeq Cluster Kit v4, this kit is not required.
  • Any Nextera libraries with any number of indexes for single-read or paired-end runs. Use the single-read kit with single-read flow cells and the paired-end kit with paired-end flow cells.
  • TruSeq HT libraries when performing a dual-indexed run on a single-read flow cell.
Kit Name Software Version
TruSeq Dual Index Sequencing Primer Box, Single Read
Catalog # FC-121-1003
TruSeq Dual Index Sequencing Primer Box, Paired End
Catalog # PE-121-1003
HCS v2.0 / RTA v1.17, or later
Sequencing primers provided in the TruSeq Dual Index Sequencing Primer Box, HP10, HP11, and HP12, replace reagents provided in the TruSeq Cluster Kit v3. Use HP10 instead of HP6 on the cBot. Use HP11 instead of HP7, and HP12 instead of HP8 on the HiSeq. For more information, see the HiSeq 1500 User Guide.

SBS Reagents

High Output


One HiSeq SBS Kit v4 or TruSeq SBS Kit v3 is required for sequencing one high output flow cell on the HiSeq. One 250-cycle kit performs up to 275 cycles of sequencing; one 200-cycle kit performs up to 209 cycles of sequencing. One 50-cycle HiSeq kit performs up to 75 cycles of sequencing; one 50-cycle TruSeq kit performs up to 58 cycles of sequencing.
Kit Name Catalog #
HiSeq SBS Kit v4 (250 cycles) FC-401-4003
HiSeq SBS Kit v4 (50 cycles) FC-401-4002
TruSeq SBS Kit v3 (200 Cycles) FC-401-3001
TruSeq SBS Kit v3 (50 Cycles) FC-401-3002

Rapid Run

One HiSeq Rapid SBS Kit v2 or TruSeq Rapid SBS Kit is required for sequencing one rapid flow cell on the HiSeq. One 500-cycle kit performs up to 525 cycles of sequencing; one 200-cycle kit performs up to 225 cycles of sequencing; one 50-cycle kit performs up to 75 cycles of sequencing.
Kit Name Catalog #
HiSeq Rapid SBS Kit v2 (500 cycles) FC-402-4023
HiSeq Rapid SBS Kit v2 (200 cycles) FC-402-4021
HiSeq Rapid SBS Kit v2 (50 cycles) FC-402-4022
TruSeq Rapid SBS Kit (200 Cycles) FC-401-4001
TruSeq Rapid SBS Kit (50 Cycles) FC-401-4002

Indexing Reagents

Indexing reagents are used for the Index Read of an indexed sequencing run. One box of indexing reagents, provided in the HiSeq and TruSeq cluster kits (PE or SR), is required for sequencing one flow cell.
Kit Name Catalog #
HiSeq SR Cluster Kit v4 GD-401-4001
HiSeq PE Cluster Kit v4 PE-401-4001
TruSeq SR Cluster Kit v3 GD-401-3001
TruSeq PE Cluster Kit v3 PE-401-3001
HiSeq Rapid SR Cluster Kit v2 GD-402-4002
HiSeq Rapid PE Cluster Kit v2 PE-402-4002
TruSeq Rapid SR Cluster Kit GD-402-4001
TruSeq Rapid PE Cluster Kit PE-402-4001

Paired-End Reagents

Paired-end reagents are used for the cluster resynthesis step in a paired-end sequencing run. One box of paired-end reagents, provided in the TruSeq and HiSeq PE cluster kits, is required for sequencing one paired-end flow cell.
Kit Name Catalog #
HiSeq PE Cluster Kit v4 PE-401-4001
TruSeq PE Cluster Kit v3 PE-401-3001
HiSeq Rapid PE Cluster Kit v2 PE-402-4002
TruSeq Rapid PE Cluster Kit PE-402-4001

Sequencing Accessories

The TruSeq Cluster Kit v3 contains an accessories kit, which includes components used for setting up a sequencing run on the HiSeq 1500.
Component Purpose
ICB Instrument Tube (for High Output Only) Used for splitting and preparing ICB.
Four flow cell gaskets Installed when loading the clustered flow cell onto the sequencing instrument.
Eight funnel caps Used to replace SBS reagent bottle caps before loading reagents onto the instrument.