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GATK HaplotypeCaller
GATK UnifiedGenotyper-3.2.2
GBS Workflow
GBS Workflow with user genome
gbsAlign_BWA 0.5.9
gbsFilter_TASSEL 3.0.133
gbsMergeSNP_TASSEL 3.0.133
gbsTags_TASSEL 3.0.133
gbsTagsToSNP_TASSEL 3.0.133
Generate detectability cartoons for syntenic features
GeneSeqer-medium (Stampede) 5.0.0
GeneSeqer_5.0
Genotype By Sequencing
Genotyping By Sequencing Workflow
GenSel
gffread-2.2.1
Gfold 1.1.1 Count
Gfold 1.1.1 Difference Expression
GLM
gmap-2018-03-25
gmap_build-2018-03-25
GNU awk
GNU grep 3.1-2
GOanna
GoSeq
Graphmap index 0.5.2
Graphmap index align 0.5.2
Graphmap owler 0.5.2
GSNAP 07.23.15
GSNAP 121212
GWASSER
Head
Heterozygote BAM to Counts
Heterozygote BAM to Counts, v1.2
Hisat2-Cuffcompare v1.0
HISAT2-index-align
HTProcess-prepare input directories 0.2
HTProcess-prepare input directories-0.1
HTProcess-prepare_directories-and-run_fastqc-0.1
HTProcess-Tophat-2.0.11 (archived)
HTProcess-Tophat-2.1.1 (archived)
HTProcess_BAMstats-1.0
HTProcess_CuffDiff-2.2.0
HTProcess_Cufflinks-2.2.0
HTProcess_Cufflinks-2.2.1
HTProcess_Cuffmerge-1
HTProcess_Cuffmerge-2.2.1
HTProcess_fastqc-0.1
HTProcess_fastqc-0.2
HTProcess_Jellyfish-2.0.0
HTProcess_Kmergenie-1.0
HTProcess_Kmergenie-1.7016
HTProcess_Tophat 2.0.13 (archived)
HTProcess_Tophat-2.0.11 (archived)
HTProcess_trimmomatic-0.33
HTProcess_trimmomatic_0.32
HTSeq-count 0.5.4
HTSeq-count-0.6.1
Htseq-Count-Merge-0.6.1
HTSeq-with-BAM-input
HTSeqQC
IDBA-UD 1.1.2
Identification of unique homozygous SNPs in mutant
IGVtools count
Index BAM file
Index BAM--get stats
Index fasta file (Samtools 1.7 faidx)
Infernal-1.1.2
InStruct
Interlace Paired FASTQ files
InterproScan 5.36.75
InterProScan_Results_Function
IUTA-1.0 in the Discovery Environment
Join multiple tab-delimited files
Kallisto
KBase data upload
khmer 3.0.0a1 extract paired reads
khmer 3.0.0a1 filter-abund
khmer 3.0.0a1 load into counting
khmer 3.0.0a1 normalize by median
KOBAS annotate 3.0.3

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HTProcess-Tophat-2.1.1 (archived)

Updated May 16, 2017

HTProcess-Tophat-2.1.1 (archived)

May 16, 2017

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