Discovery Environment Applications List

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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
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LASTAL-8.69
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LASTDB-8.69
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LD (Tassel4)
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Linux stream editor
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List contents of FAST5 file(s)
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LncTar-1.0
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MACS
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MAFFT 7.0.17
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Make new names for fasta sequences
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maker2jbrowse
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maker2zff
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Mapping illumina seq data Part 1
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MaxBin 2.2 in the Discovery Environment
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Medusa-1.6
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Megahit-1.0.6
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Meraculous 2.2.6
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Merge BAM files
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Merge SFF files-2.9
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Merge_htseq_count-1.0
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MergeG2P 0.0.2
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MERRA-AS instM_3d_ana_Np (Analyzed State, Meteorology Instantaneous Monthly)
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MERRA-AS tavg1_2d_lnd_Nx (Land related surface quantities)
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MetaGeneAnnotator-1.0.0
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MetaGeneMark GFF to IGB
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MetaPhyler-SR 0.115
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MetaQUAST-4.0 (denovo based) in DE
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MetaQUAST-4.0 (reference based) in DE
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MetaQUAST-4.3 (denovo based) in DE
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MetaQUAST-4.3 (reference based) in DE
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Mikado
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Miniasm 0.2_r168
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Minimap2_index-2.10
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Minimap2_index_align-2.10
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miRanda 3.3a
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miRDeep2 2.0.0.8
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miRDeep2 2.0.0.8 mapper
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miRDeep2 2.0.0.8 quantifier
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MLM 4.3.13
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MLM (Tassel4)
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MLM Workflow
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MLMM 0.0.2
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Modify_GFF_coordinates
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Molecular Dating with Penalized Likelihood
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mpileup
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MrBayes on CyVerse UK
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MrBayes_mpi_basic-3.2.3
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MUSCLE
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MUSCLE-3.8.31 on Stampede
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Mutant Identification 1
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mutant interval identification
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nanofilt 2.5.0
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Nanopolish vcf2fasta 0.10.2
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Nanopolish-call-methylation-0.10.2
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Nanopolish-eventalign-0.7.1
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Nanopolish-eventalign-0.10.2
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Nanopolish-extract-0.8.1
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Nanopolish-extract-0.10.2
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Nanopolish-index-0.8.1
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Nanopolish-index-0.10.2
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Nanopolish-variants-0.10.2
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nanoqc 0.91
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NCBI GenBank Import
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NCBI SRA Import
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NCBI SRA Import 1.2
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NCBI SRA Submission - BioProject Creation
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NCBI SRA Submission - BioProject Update
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NCBI SRA Submission Report Retrieval
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NCBI SRA to Solid Format (abi-dump)
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NCBI SRA Toolkit fastq-dump 2.1.9
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NCBI SRA Toolkit fastq-dump 2.3.4
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NCBI SRA Toolkit fastq-dump 2.8.1
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Newbler
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Newbler 2.6.0
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Ninja
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non-unique filter
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Normalize By Median
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NPUTE-0.0.1
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Numeric Evaluation of a Data Column
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NumericalTransform 4.3.14
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Oases 0.2.08
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Ontologizer
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OposSOM-2.0.1-biomart
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OrthoMCL v1.4
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Discovery Environment Applications List

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Linux stream editor

Owned by de-confluence

Last updated: Jul 29, 2016 by Roger Barthelson

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