Discovery Environment Applications List

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Peak Ranger_wig_1.18
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Peak Ranger_wigpe_1.18
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PEAR-0.9.6
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PepMOD
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PGDSpider tool for data conversion
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Photometry-pipeline-v1.0
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PhyML
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Picard Preprocess-1.98
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Picard-MarkDuplicates-2.7.1 in the Discovery Environment
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pigz-2.3.4 (Compress multiple files with gzip parallely)
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PK Unzip
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Platypus-0.7.9.5
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PLINK
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PLINK 1.90b4
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PLINK 1.90b4 Conversion
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PLINK 2 AntEpiSeeker Conversion
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PLINK Conversion
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Polymarker
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population genomics analysis flow
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Porechop 0.2.3
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Poretools combine 0.6.1a1
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Poretools events 0.6.1a1
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Poretools fasta 0.6.1a1
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Poretools fastq 0.6.1a1
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Poretools index 0.6.1a1
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Poretools metadata 0.6.1a1
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Poretools nucdist 0.6.1a1
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Poretools qualdist 0.6.1a1
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Poretools readstats 0.6.1a1
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Poretools stats 0.6.1a1
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Poretools times 0.6.1a1
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Poretools winner 0.6.1a1
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Principal Component Analysis
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Prinseq-Graph-noPCA evaluate reads
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Prinseq-lite
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Prodigal
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ProgressiveMauve
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PROML
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PROTNJ
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PROTPARS
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QIIME-1.9.1 in Discovery Environment
QTL Cartographer
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QTL simulation workflow
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QUAST (3.2 and 4.0) in the Discovery Environment
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queryOrthoMCL 1.0
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Rascaf V1.0.2 in Discovery Environment
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RAxML on CyVerse UK
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RAxML-7.3.0
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RAxML-8.2.3_small_and_medium
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raxml-RFdistance-8.2.11
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Ray-2.3.1
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Rename contigs 2.0
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rePair-Fix Read Pairing
RMTA v2.6.3
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rnaQUAST 1.2.0 (reference based) using DE
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rnaQUAST_1.2.0 (de novo based)
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RSEM 1.2.12
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RSEM-Prepare-Reference 1.2.19
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RseqFilt-1.0
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Sabre-barcode-demultiplexing
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Sailfish_align_quant-0.9.2
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salmon-index-quant-0.8.1
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SAM to sorted BAMv2
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SAM_to_Sorted_BAM-0.1.9
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Samtools 1.7 BAM to SAM
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Samtools 1.7 bamtofastq
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Samtools 1.7 flagstat
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Samtools 1.7 Index BAM file
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SAMTools 1.7 mpileup
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Samtools 1.7 rmdup + flagstat
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Samtools 1.7 rmdup remove PCR duplicates
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Samtools 1.7 SAM to BAM format conversion
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SAMTools 1.7 SAM to sorted BAM
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Samtools 1.7 Sort Bam file
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Samtools 1.7 view - Filter mapped or unmapped reads
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SAMTools 1.7 view Filter by region
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Samtools faidx (fasta indexer)
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SAMtools index BAM file
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SAMtools view-BEDtools bamtoFastq
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SAMTOOLS-0.1.19 mpileup raw-vcf-out
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SAMTOOLS-0.1.19 mpileup variant pipeline
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BCFTOOLS-1.13 VCF-Utilities varFilter
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Samtools_mapping_stats-1.0
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Scrappie
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Scythe-0.991 using DE
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Select contigs
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seqtk_seq-1.0.76
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SequenceLogo
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Seurat VICE app in DE
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Sff2Fastq
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SGA 0.10.15 Pre-Process Reads
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Sickle-quality-based-trimming version 1.0
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SKAT
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Sleuth
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Snap, gene prediction
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Snap-gene prediction-112913
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SnapATAC VICE app in DE
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SNP calling illumina seq data Part 2
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snp_ase
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Soapdenovo
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Soapdenovo 2.04
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Soapdenovo-Trans 1.0
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Soapdenovo-trans-small-1.0.4
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Sort a File On A Column
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Sort File On 2 columns
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SPAdes-3.8.0
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Spladder-1.0.0
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Split FASTA file
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SRA-Import-0.1.0
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Sspace
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Stampy-build-and-map
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Star-index-align_2.5.3.a
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STAR_2.4.0.1
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STAR_2.4.0.1_GenerateGenomeIndex
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StringTie1.3.3
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StringTie-1.3.3_merge
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Structure2Tassel
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Suffixerator
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Synapse_client-1.6.1
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Syntenic_Feature_Detector
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taco-0.7.0
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Tassel3 Conversion
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Tassel4 Conversion
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tbl2asn (gapped)-22.9 using DE
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tbl2asn (gapped)-25.8 using DE
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tbl2asn (ungapped)-22.9 using DE
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tbl2asn (ungapped)-25.8 using DE
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TIES baseline 1 - averaging
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TIES baseline 2 - line fitting
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TIES basic complete run (rev A)
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TIES step 1 - parse input CSV data
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TIES step 2 - training full LSS model
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tophat2gff3
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Transcript decoder 1.0
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Transcript decoder 2.0
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TransDecoder 5.5.0
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TransDecoder 5.5.0 detect coding regions
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TransDecoder 5.5.0 extract long ORFs
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TreeView
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trim_galore-0.4.1 using DE
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Trimmomatic-programmable-0.33
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Trimmomatic-programmable-0.36
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Trimmomatic-programmable-0.38
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Trinity normalize by k-mer coverage r11.10.13
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Trinity r2013-08-14a
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Trinity r2013-11-10
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Trinity-64GB-2.1.1
Tuxedo suite PE up to 4 conditions
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Uncompress files with gunzip 1.6-2
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Uncompress with gunzip
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Uncompress with tar
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UNEAK
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unique filter
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unpigz-2.3.4 (Uncompress multiple files with ungzip parallely)
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Validate
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Variable Region Identifier and Remover
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Variant annotation using SnpEff in DE
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VarScan-2.3.6 SNP caller
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VCF to GFF3
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vcfutils.pl varFilter
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vContact_0.1.49 and vContact-PCs

Discovery Environment Applications List

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List of Applications

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SAMTOOLS-0.1.19 mpileup variant pipeline

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