Software Components

16S Metagenomics App

Software

Version

Isas (Analysis Software)

2.0.5.35.6

Amplicon DS v1.2 App

Software

Version

Isas (Analysis Software)

2.5.40.16

SAMtools

0.1.10-isis-1.0.3

Somatic Variant Caller 3.5.2.1
Illumina Annotation Service (IAS) 3.0
Annotation Dataset 72.5

BWA Enrichment App

Software

Version

BWA 0.7.7-isis-1.0.0

GATK

1.6.23-gf0210b3

Picard

1.79

SAMtools 0.1.19-isis-1.0.1
Illumina Annotation Service (IAS) 3.0
Tabix 0.2.5 (r1005)

Cufflinks Assembly & DE v2.0 App

Software

Version

Isas (Analysis Software)

2.6.25.12

Bedtools

2.17.0

Cufflinks 2.2.1
BLAST 2.2.26+

Enrichment App v3.0

Software

Version

Isas (Analysis Software)

2.10.11

Isaac (Aligner)

03.16.02.20

Starling (Variant Caller) 2.4.6
Pisces (Somatic Variant Caller) 5.1.3.60
Manta (Structural Variant Caller) 0.28.0
Canvas (Copy Number Variant Caller) 1.13.0
Illumina Annotation Engine 1.3.5.2
SAMtools 1.2
Picard (Calculate HS Metrics) 1.130
PUMA Metrics 1.0.13.0

Isaac Whole Genome Sequencing v4.0 App

Software

Version

Isas (Analysis Software)

2.5.55.16

Isaac (Aligner)

SAAC00776.15.01.27

Starling Variant Caller starka-2.1.4.2
SAMtools 0.1.19-isis-1.0.3
Manta (Structural Variant Caller) 0.23.1
Canvas (Copy Number Variant Caller) 1.1.0.5
Tabix 0.2.6

MethylSeq App

Software

Version

Isas (Analysis Software)

2.5.61.0

Bismark

0.12.2

Bowtie2 2.2.2
SAMtools 0.1.19-isis-1.0.3

mtDNA Variant Processor App

Software

Version

Isas (Analysis Software)

2.6.7.4
BWA-MEM (Aligner) 0.7.9

RNA Express App

Software

Version

STAR (Aligner)

2.3.1s
DE-Seq (Software Analysis) 1.0.17

RNA-Seq Alignment App

Software

Version

Isas (Analysis Software)

2.6.25.11

Isaac Variant Caller

2.3.13.31-g3c98c29

STAR (Aligner) 2.5.0a
TopHat (Aligner) 2.1.0
Bowtie 0.12.9
Bowtie2 2.2.6
IONA (Annotation Service) 1.0.10.37
BEDtools 2.17.0
Cufflinks 2.2.1
BLAST 2.2.26+

Small RNA App

Software

Version

Isas (Analysis Software)

2.5.52.11
SAMtools 0.1.19-isis-1.0.2

MiRDeep

3.2

Bowtie 0.12.8
DESeq2 1.0.17

TopHat Alignment and Cufflinks Assembly & DE v1.0 App

Software

Version

TopHat2

2.0.7
Bowtie 0.12.9

Cufflinks

2.1.1

Isaac Variant Caller 2.0.5
Picard 1.72

TruSeq Amplicon v2.0 App

Software

Version

Isis (Analysis Software)

2.6.21.7

SAMtools 1.2
Somatic Variant Caller 4.0.13.1
Starling (Isaac Variant Caller) 2.1.4.1
GATK (Variant Caller) 1.6-23-gf0210b3
Illumina On-Node Annotation (IONA) 1.0.10.37
MarkDuplicates 1.0.1
mono 3.12.1

TruSeq Targeted RNA App

Software

Version

Isas (Analysis Software)

2.5.57.4.TREx
Scipy 0.14.0

Pandas

0.14.1

SAMtools 0.1.19-isis-1.0.3

TruSeq Long-Read Assembly App

Software

Version

Tornado

2.0
BWA 0.6.2

SGA

0.0.37

SAMtools 0.1.18
Khmer (Coverage Normalization) 0.2

TruSeq Phasing Analysis App

Software

Version

Prism 2.2

BEDTools

2.17.0
BWA 0.7.5a

Tabix

0.2.5

SAMtools 0.1.18
VCFtools 0.1.10

TruSight Tumor 15 App

Software

Version

Isas (Analysis Software)

2.6.2.3
Somatic Variant Caller 4.0.7.6

Illumina Annotation Engine (IAE)

1.1.8.0

Tumor Normal v5.0 App

Software

Version

Strelka (Somatic Variant Caller) 

2.8.0

Manta (Structural Variant Caller) 

1.1.1

Canvas (Copy Number Variant Caller)  1.28.0.272
Illumina Annotation Engine 1.6.2