Discovery Environment Applications List

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BCFtools 1.8 call
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BCFtools 1.8 index
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BCFtools 1.8 merge VCF
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BCFtools 1.8 view
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BEAST2 on CyVerse UK
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BEAST on CyVerse UK
BEAST-2.1.3
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BEDTools 2.26 fastaFromBed
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BEDTools 2.26 slopBed
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BEDTools 2.26.0 bamToBed
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BEDTools 2.26.0 intersectBed
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BEDTOOLS BAMtoFastq-2.26
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BEDTools coverageBed
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Bedtools Genome Coverage-BAM-2.26
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BEDTools genomeCoverageBed
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BEDTools maskFastaFromBed
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Best Hit for Blat Output
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Bismark
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Bismark Genome Preparation
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Bismark Methylation Extractor
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Blast2Seqs
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Blastdbcmd-batch-2.6.0
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Blastdbcmd-single-2.6.0
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Blastn-2.2.26
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Blastn-2.6.0+
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BLASTp UniProt
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Blastp-2.2.29
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Blastp-2.6.0+
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BLASTX (HPC)
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blat 36 (with options)
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Blat (default)
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BLAT_psl_to_SAM
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Blat_with_BAM_output
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Bowtie2-2.2.4 Bowtie2-Build indexer and aligner (HPC)
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Bowtie2Build-2.2.4 indexer
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Bowtie 1.2.2 build and map
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Bowtie-2.2.1--Build-and-Map
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Bowtie-Build
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btrim
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BuildICM-1.0.0-Dev
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Bulk Blast 2 Sequences
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BUSCO in the Discovery Environment
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BUSCO-v2.0 in the Discovery Environment
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BUSCO-v3.0 in the Discovery Environment
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BWA 0.7.4 Divergent species
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BWA 0.7.12 indexer aligner and mem (HPC)
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BWA Aligner for Paired-End Illumina Reads
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BWA Aligner for Single-End Illumina Reads
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BWA aln 0.7.4
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BWA index 0.7.4
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BWA mem 0.7.15
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BWA-0.7.4 non-model species
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BWA_mem_longreads-0.7.15
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bzip2 and bunzip2
CACE
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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

Discovery Environment Applications List

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Convert SAM-to-sorted-BAM

Owned by de-confluence

Last updated: Jun 29, 2016 by Roger Barthelson

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