Discovery Environment Applications List

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Cufflinks_from_SAM-2.2.1 in DE
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Cuffmerge2
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Cuffmerge 2.2.1
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curl-7.45.0
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Cut Columns
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cutadapt
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DataHog
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de novo population genomics analysis
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De-interlace paired fasta
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DeltaBLAST-2.2.29+
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DESeq
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DESeq2
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DESeq2 (multifactorial pairwise comparisons)
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DIAMOND 0.9.10
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DIAMOND-makedb-0.9.10
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DNANJ
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DNAPARS
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dos2unix
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Downsample reads
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draw Venn diagrams
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DREME 5.0.5
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DynamicTrim
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edgeR (multifactorial pairwise comparisons) in DE
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edgeR with Fisher's Exact Test
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EMBOSS Cusp
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EMBOSS Seqret
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Emboss transeq
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Enhanced R Script
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evolinc
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Evolinc in the Discovery Environment
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Evolinc_merge-1.0
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Extract First Lines From a File
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Extract Last Lines From a File
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FALCON (Small Genomes) 0.4.2
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FALCON-formatter
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FaST-LMM Results Plotter 2
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FaST-LMM Reults Plotter 2
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FaST-LMM-2.07
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FASTA Minimum Size Filter
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fastaRename
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FastLMM Result Plotter
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Fastq-Join
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Fastq-Sample-0.8
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Fastq-screen-0.4.4
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Fastq-screen-0.11.1
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FASTQ_SHRINKER
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FastQC
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FastQC 0.10.1 (multi-file)
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FastQC (demo)
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FastQC-0.11.5 (multi-file)
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FastQC-plus 0.10.1 (multi-file)
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fastqCombinePariedEnd
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FastTree2
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FastTree Dispatcher 2.1.4
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FASTX Barcode Splitter
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FASTX Clipper 0.0.14
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Fastx Collapser
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FASTX fastq quality filter 0.0.14
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FASTX fastq to fasta 0.0.14
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FASTX quality filter and trim
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FASTX Quality Trimmer
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FASTX Toolkit
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FASTX Trimmer 0.0.14
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File_Select v1.0
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File_Split v1.0
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Filter homozygous SNPs
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filter pileup
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Filter_CuffDiff_Results
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Final filter
Final filter2
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Find Lines Matching a Regular Expression
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Find SNPS - mpileup
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flattenClusters 1.0
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Fluorescent Imaging Pipeline (FLIP)
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Freebayes-0.9.20
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GapCloser 1.12
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GATK CombineGCVFs-3.2.2
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GATK GenotypeGVCFs-3.2.2
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GATK HaplotypeCaller
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GATK UnifiedGenotyper-3.2.2
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GBS Workflow
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GBS Workflow with user genome
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gbsAlign_BWA 0.5.9
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gbsFilter_TASSEL 3.0.133
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gbsMergeSNP_TASSEL 3.0.133
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gbsTags_TASSEL 3.0.133
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gbsTagsToSNP_TASSEL 3.0.133
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Generate detectability cartoons for syntenic features
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GeneSeqer-medium (Stampede) 5.0.0
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GeneSeqer_5.0
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Genotype By Sequencing
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Genotyping By Sequencing Workflow
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GenSel
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gffread-2.2.1
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Gfold 1.1.1 Count
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Gfold 1.1.1 Difference Expression
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GLM
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gmap-2018-03-25
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gmap_build-2018-03-25
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GNU awk
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GNU grep 3.1-2
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GOanna
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GoSeq
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Graphmap index 0.5.2
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Graphmap index align 0.5.2
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Graphmap owler 0.5.2
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GSNAP 07.23.15
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GSNAP 121212
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GWASSER
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Head
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Heterozygote BAM to Counts
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Heterozygote BAM to Counts, v1.2
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Hisat2-Cuffcompare v1.0
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HISAT2-index-align
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HTProcess-prepare input directories 0.2
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HTProcess-prepare input directories-0.1
HTProcess-prepare_directories-and-run_fastqc-0.1
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HTProcess-Tophat-2.0.11 (archived)
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HTProcess-Tophat-2.1.1 (archived)
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HTProcess_BAMstats-1.0
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HTProcess_CuffDiff-2.2.0
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HTProcess_Cufflinks-2.2.0
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HTProcess_Cufflinks-2.2.1
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HTProcess_Cuffmerge-1
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HTProcess_Cuffmerge-2.2.1
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HTProcess_fastqc-0.1
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HTProcess_fastqc-0.2
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HTProcess_Jellyfish-2.0.0
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HTProcess_Kmergenie-1.0
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HTProcess_Kmergenie-1.7016
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HTProcess_Tophat 2.0.13 (archived)
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HTProcess_Tophat-2.0.11 (archived)
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HTProcess_trimmomatic-0.33
HTProcess_trimmomatic_0.32
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HTSeq-count 0.5.4
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HTSeq-count-0.6.1
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Htseq-Count-Merge-0.6.1
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HTSeq-with-BAM-input
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HTSeqQC
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IDBA-UD 1.1.2
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Identification of unique homozygous SNPs in mutant
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IGVtools count
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Index BAM file
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Index BAM--get stats
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Index fasta file (Samtools 1.7 faidx)
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Infernal-1.1.2
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InStruct
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Interlace Paired FASTQ files
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InterproScan 5.36.75
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InterProScan_Results_Function
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IUTA-1.0 in the Discovery Environment
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Join multiple tab-delimited files
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Kallisto
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KBase data upload
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khmer 3.0.0a1 extract paired reads
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khmer 3.0.0a1 filter-abund
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khmer 3.0.0a1 load into counting
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khmer 3.0.0a1 normalize by median
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KOBAS annotate 3.0.3
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KOBAS annotate and identify 3.0.3
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KOBAS identify 3.0.3

Discovery Environment Applications List

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GBS Workflow

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Last updated: Sept 17, 2013 by NicoleHVersion comment

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