Discovery Environment Applications List

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Calling SNPs INDELs with SAMtools BCFtools
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Canberra Distance
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Canu 1.8
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CD-HIT-est 4.6.8
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CEGMA
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CharaParser Learn
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CharaParser Markup
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Check covariance matrix file (CheckCvm)
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Check standard GWAS files (CheckGwas)
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Chromatra L
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Chromatra T
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Clean_fasta_header
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ClustalW2
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clusterProfiler
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clusterReport
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CNVnator-0.3.3
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combine GAFs
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Compress a directory with GNU tar-1.27.1
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Compress files with gzip 1.6-2
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Compress selected files with GNU tar
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Compute Contig Statistics
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Concatenate 2 Files-workflow edition.
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Concatenate Multiple Files
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construction genetic map
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Convert bwt to arf
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Convert SAM-to-sorted-BAM
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ConvertTraitID 0.0.1
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Copy with Scaffolding XML of DESeq2 (multifactorial pairwise comparisons)
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Create BLAST database
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Create BLAST database-2.6.0+
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create dir
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Create_BLAST_database-2.6.0__with_parse_seqids_option
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Cuffcompare-2.2.1
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Cuffdiff
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Cuffdiff2
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Cuffdiff2 with JS option
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Cuffdiff2-16-way-max
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CuffDiff 2.2.1a
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Cufflinks
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Cufflinks 2.2.1
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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

Discovery Environment Applications List

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FastLMM Result Plotter

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Last updated: Jul 06, 2016 by Roger Barthelson