Discovery Environment Applications List

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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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PAGE
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PAML
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ParaAT 2.0
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parallel-fastq-dump-0.6.1
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parallel-fastq-dump-multi-0.6.5
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Parse Blast Report
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parseBlastBpo
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Parser-3.0.20
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PcPipe 1.0.0
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Peak Ranger
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Peak Ranger_ranger_1.18
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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

Discovery Environment Applications List

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List of Applications

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Oases 0.2.08

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Last updated: Sept 09, 2015 by Roger Barthelson