The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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Page: AAARF v 1.0.1 Page: add column to file Page: add column to file2 Page: Add GO to Blastp-uniprot output Page: Admixture Page: AgBase GOanna 2.1 Page: ALLMAPS Page: ALLMAPS merge Page: ALLMAPS path Page: AllpathsLG 44837 Page: AllpathsLG-small-genomes-44837 Page: Annotate transcripts Page: AntEpiSeeker 2.0 Page: appendUnclustered Page: Assembly Stats (assemblathon tool) Page: Assess Assembly vs whole genome Page: Bam to Counts (general) Page: BAM to Counts (named outputs) Page: bayesembler-1.2 Page: Bayesian BiClustering Page: BCFtools 1.8 call Page: BCFtools 1.8 index Page: BCFtools 1.8 merge VCF Page: BCFtools 1.8 view Page: BEAST2 on CyVerse UK Page: BEAST-2.1.3 Page: BEAST on CyVerse UK Page: BEDTools 2.26.0 bamToBed Page: BEDTools 2.26.0 intersectBed Page: BEDTools 2.26 fastaFromBed Page: BEDTools 2.26 slopBed Page: BEDTOOLS BAMtoFastq-2.26 Page: BEDTools coverageBed Page: Bedtools Genome Coverage-BAM-2.26 Page: BEDTools genomeCoverageBed Page: BEDTools maskFastaFromBed Page: Best Hit for Blat Output Page: Bismark Page: Bismark Genome Preparation Page: Bismark Methylation Extractor Page: Blast2Seqs Page: Blastdbcmd-batch-2.6.0 Page: Blastdbcmd-single-2.6.0 Page: Blastn-2.2.26 Page: Blastn-2.6.0+ Page: Blastp-2.2.29 Page: Blastp-2.6.0+ Page: Blastp of a subset of uniprot Page: BLASTX (HPC) Page: blat 36 (with options) Page: BLAT_psl_to_SAM Page: Blat_with_BAM_output Page: Blat (default) Page: Bowtie2-2.2.4 Bowtie2-Build indexer and aligner (HPC) Page: Bowtie2Build-2.2.4 indexer Page: Bowtie 1.2.2 build and map Page: Bowtie-2.2.1--Build-and-Map Page: Bowtie-Build Page: btrim Page: BuildICM-1.0.0-Dev Page: Bulk Blast 2 Sequences Page: BUSCO in the Discovery Environment Page: BUSCO-v2.0 in the Discovery Environment Page: BUSCO-v3.0 in the Discovery Environment Page: BWA 0.7.4 Divergent species Page: BWA 0.7.12 indexer aligner and mem (HPC) Page: BWA-0.7.4 non-model species Page: BWA_mem_longreads-0.7.15 Page: BWA Aligner for Paired-End Illumina Reads Page: BWA Aligner for Single-End Illumina Reads Page: BWA aln 0.7.4 Page: BWA index 0.7.4 Page: BWA mem 0.7.15 Page: bzip2 and bunzip2 Page: CACE Page: Calling SNPs INDELs with SAMtools BCFtools Page: Canberra Distance Page: Canu 1.7 Page: CD-HIT-est 4.6.8 Page: CEGMA Page: CharaParser Learn Page: CharaParser Markup Page: Check covariance matrix file (CheckCvm) Page: Check standard GWAS files (CheckGwas) Page: Chromatra L Page: Chromatra T Page: Clean_fasta_header Page: ClustalW2 Page: clusterReport Page: CNVnator-0.3.3 Page: Compress a directory with GNU tar-1.27.1 Page: Compress files with gzip 1.6-2 Page: Compress selected files with GNU tar Page: Compute Contig Statistics Page: Concatenate 2 Files-workflow edition. Page: Concatenate Multiple Files Page: construction genetic map Page: Convert bwt to arf Page: Convert SAM-to-sorted-BAM Page: ConvertTraitID 0.0.1 Page: Copy with Scaffolding XML of DESeq2 (multifactorial pairwise comparisons) Page: Create_BLAST_database-2.6.0__with_parse_seqids_option Page: Create BLAST database Page: Create BLAST database-2.6.0+ Page: create dir Page: Cuffcompare-2.2.1 Page: Cuffdiff Page: Cuffdiff2 Page: Cuffdiff2-16-way-max Page: Cuffdiff2 with JS option Page: CuffDiff 2.2.1a Page: Cufflinks Page: Cufflinks 2.2.1 Page: Cufflinks_from_SAM-2.2.1 in DE Page: Cuffmerge2 Page: Cuffmerge 2.2.1 Page: curl-7.45.0 Page: cutadapt Page: Cut Columns Page: De-interlace paired fasta Page: DeltaBLAST-2.2.29+ Page: de novo population genomics analysis Page: DESeq Page: DESeq2 Page: DESeq2 (multifactorial pairwise comparisons) Page: DNANJ Page: DNAPARS Page: dos2unix Page: Downsample reads Page: draw Venn diagrams Page: DREME Page: DynamicTrim Page: edgeR (multifactorial pairwise comparisons) in DE Page: edgeR with Fisher's Exact Test Page: EMBOSS Cusp Page: EMBOSS Seqret Page: Emboss transeq Page: Enhanced R Script Page: evolinc Page: Evolinc_merge-1.0 Page: Evolinc in the Discovery Environment Page: Extract First Lines From a File Page: Extract Last Lines From a File Page: FALCON (Small Genomes) 0.4.2 Page: FALCON-formatter Page: FASTA Minimum Size Filter Page: fastaRename Page: FaST-LMM-2.07 Page: FastLMM Result Plotter Page: FaST-LMM Results Plotter 2 Page: FaST-LMM Reults Plotter 2 Page: FASTQ_SHRINKER Page: FastQC Page: FastQC 0.10.1 (multi-file) Page: FastQC-0.11.5 (multi-file) Page: FastQC (demo) Page: fastqCombinePariedEnd Page: FastQC-plus 0.10.1 (multi-file) Page: Fastq-Join Page: Fastq-screen-0.4.4 Page: Fastq-screen-0.11.1 Page: FastTree2 Page: FastTree Dispatcher 2.1.4 Page: FASTX Barcode Splitter Page: FASTX Clipper 0.0.14 Page: Fastx Collapser Page: FASTX fastq quality filter 0.0.14 Page: FASTX fastq to fasta 0.0.14 Page: FASTX quality filter and trim Page: FASTX Quality Trimmer Page: FASTX Toolkit Page: FASTX Trimmer 0.0.14 Page: Filter_CuffDiff_Results Page: Filter homozygous SNPs Page: filter pileup Page: Final filter Page: Final filter2 Page: Find Lines Matching a Regular Expression Page: Find SNPS - mpileup Page: flattenClusters 1.0 Page: Freebayes-0.9.20 Page: GapCloser 1.12 Page: GATK CombineGCVFs-3.2.2 Page: GATK GenotypeGVCFs-3.2.2 Page: GATK HaplotypeCaller Page: GATK UnifiedGenotyper-3.2.2 Page: gbsAlign_BWA 0.5.9 Page: gbsFilter_TASSEL 3.0.133 Page: gbsMergeSNP_TASSEL 3.0.133 Page: gbsTags_TASSEL 3.0.133 Page: gbsTagsToSNP_TASSEL 3.0.133 Page: GBS Workflow Page: GBS Workflow with user genome Page: Generate detectability cartoons for syntenic features Page: GeneSeqer_5.0 Page: GeneSeqer-medium (Stampede) 5.0.0 Page: Genotype By Sequencing Page: Genotyping By Sequencing Workflow Page: GenSel Page: gffread-2.2.1 Page: Gfold 1.1.1 Count Page: Gfold 1.1.1 Difference Expression Page: GLM Page: GMAP-7.23.15 Page: GNU awk Page: GNU grep 3.1-2 Page: GoSeq Page: GSNAP 07.23.15 Page: GSNAP 121212 Page: GWASSER Page: Head Page: Heterozygote BAM to Counts Page: Heterozygote BAM to Counts, v1.2 Page: Hisat2-Cuffcompare v1.0 Page: HISAT2-index-align Page: HTProcess_BAMstats-1.0 Page: HTProcess_CuffDiff-2.2.0 Page: HTProcess_Cufflinks-2.2.0 Page: HTProcess_Cufflinks-2.2.1 Page: HTProcess_Cuffmerge-1 Page: HTProcess_Cuffmerge-2.2.1 Page: HTProcess_fastqc-0.1 Page: HTProcess_fastqc-0.2 Page: HTProcess_Jellyfish-2.0.0 Page: HTProcess_Kmergenie-1.0 Page: HTProcess_Kmergenie-1.7016 Page: HTProcess_Tophat 2.0.13 (archived) Page: HTProcess_Tophat-2.0.11 (archived) Page: HTProcess_trimmomatic-0.33 Page: HTProcess_trimmomatic_0.32 Page: HTProcess-prepare_directories-and-run_fastqc-0.1 Page: HTProcess-prepare input directories 0.2 Page: HTProcess-prepare input directories-0.1 Page: HTProcess-Tophat-2.0.11 (archived) Page: HTProcess-Tophat-2.1.1 (archived) Page: HTSeq-count 0.5.4 Page: HTSeq-count-0.6.1 Page: HTSeq-with-BAM-input Page: IDBA-UD 1.1.2 Page: Identification of unique homozygous SNPs in mutant Page: IGVtools count Page: Index BAM file Page: Index BAM--get stats Page: Index fasta file (Samtools 1.7 faidx) Page: InStruct Page: Interlace Paired FASTQ files Page: InterproScan 5.17.56 Page: InterProScan_Results_Function Page: IUTA-1.0 in the Discovery Environment Page: Join multiple tab-delimited files Page: Kallisto Page: KBase data upload Page: khmer 3.0.0a1 extract paired reads Page: khmer 3.0.0a1 filter-abund Page: khmer 3.0.0a1 load into counting Page: khmer 3.0.0a1 normalize by median Page: LASTAL-8.69 Page: LASTDB-8.69 Page: LD (Tassel4) Page: Linux stream editor Page: MACS Page: MAFFT 7.0.17 Page: Make new names for fasta sequences Page: maker2jbrowse Page: maker2zff Page: Mapping illumina seq data Part 1 Page: MaxBin 2.2 in the Discovery Environment Page: Medusa-1.6 Page: Megahit-1.0.6 Page: Merge_htseq_count-1.0 Page: Merge BAM files Page: MergeG2P 0.0.2 Page: Merge SFF files-2.9 Page: MERRA-AS instM_3d_ana_Np (Analyzed State, Meteorology Instantaneous Monthly) Page: MERRA-AS tavg1_2d_lnd_Nx (Land related surface quantities) Page: MetaGeneAnnotator-1.0.0 Page: MetaGeneMark GFF to IGB Page: MetaPhyler-SR 0.115 Page: MetaQUAST-4.0 (denovo based) in DE Page: MetaQUAST-4.0 (reference based) in DE Page: MetaQUAST-4.3 (denovo based) in DE Page: MetaQUAST-4.3 (reference based) in DE Page: Mikado Page: Miniasm 0.2_r168 Page: Minimap2_index-2.10 Page: Minimap2_index_align-2.10 Page: miRanda 3.3a Page: miRDeep2 2.0.0.8 Page: miRDeep2 2.0.0.8 mapper Page: miRDeep2 2.0.0.8 quantifier Page: MLM 4.3.13 Page: MLM (Tassel4) Page: MLMM 0.0.2 Page: MLM Workflow Page: Modify_GFF_coordinates Page: Molecular Dating with Penalized Likelihood Page: mpileup Page: MrBayes_mpi_basic-3.2.3 Page: MrBayes on CyVerse UK Page: MUSCLE Page: MUSCLE-3.8.31 on Stampede Page: Mutant Identification 1 Page: mutant interval identification Page: Nanopolish-call-methylation-0.10.2 Page: Nanopolish-eventalign-0.7.1 Page: Nanopolish-eventalign-0.10.2 Page: Nanopolish-extract-0.8.1 Page: Nanopolish-extract-0.10.2 Page: Nanopolish-index-0.8.1 Page: Nanopolish-index-0.10.2 Page: Nanopolish-variants-0.10.2 Page: Nanopolish vcf2fasta 0.10.2 Page: NCBI GenBank Import Page: NCBI SRA Import Page: NCBI SRA Import 1.2 Page: NCBI SRA Submission - BioProject Creation Page: NCBI SRA Submission - BioProject Update Page: NCBI SRA Submission Report Retrieval Page: NCBI SRA Toolkit fastq-dump 2.1.9 Page: NCBI SRA Toolkit fastq-dump 2.3.4 Page: NCBI SRA Toolkit fastq-dump 2.8.1 Page: NCBI SRA to Solid Format (abi-dump) Page: Newbler Page: Newbler 2.6.0 Page: Ninja Page: non-unique filter Page: Normalize By Median Page: NPUTE-0.0.1 Page: NumericalTransform 4.3.14 Page: Numeric Evaluation of a Data Column Page: Oases 0.2.08 Page: Ontologizer Page: OrthoMCL v1.4 Page: PAGE Page: PAML Page: ParaAT 2.0 Page: parallel-fastq-dump-0.6.1 Page: parseBlastBpo Page: Parse Blast Report Page: Parser-3.0.20 Page: PcPipe 1.0.0 Page: Peak Ranger Page: Peak Ranger_ranger_1.18 Page: Peak Ranger_wig_1.18 Page: Peak Ranger_wigpe_1.18 Page: PEAR-0.9.6 Page: PepMOD Page: PGDSpider tool for data conversion Page: Photometry-pipeline-v1.0 Page: PhyML Page: Picard-MarkDuplicates-2.7.1 in the Discovery Environment Page: Picard Preprocess-1.98 Page: pigz-2.3.4 (Compress multiple files with gzip parallely) Page: PK Unzip Page: Platypus-0.7.9.5 Page: PLINK Page: PLINK 1.90b4 Page: PLINK 1.90b4 Conversion Page: PLINK 2 AntEpiSeeker Conversion Page: PLINK Conversion Page: Polymarker Page: population genomics analysis flow Page: Principal Component Analysis Page: Prinseq-Graph-noPCA evaluate reads Page: Prinseq-lite Page: Prodigal Page: ProgressiveMauve Page: PROML Page: PROTNJ Page: PROTPARS Page: QIIME-1.9.1 in Discovery Environment Page: QTL Cartographer Page: QTL simulation workflow Page: QUAST (3.2 and 4.0) in the Discovery Environment Page: queryOrthoMCL 1.0 Page: Rascaf V1.0.2 in Discovery Environment Page: RAxML-7.3.0 Page: RAxML-8.2.3_small_and_medium Page: RAxML on CyVerse UK Page: raxml-RFdistance-8.2.11 Page: Ray-2.3.1 Page: Rename contigs 2.0 Page: rePair-Fix Read Pairing Page: rnaQUAST 1.2.0 (reference based) using DE Page: rnaQUAST_1.2.0 (de novo based) Page: RSEM 1.2.12 Page: RSEM-Prepare-Reference 1.2.19 Page: Sabre-barcode-demultiplexing Page: Sailfish_align_quant-0.9.2 Page: salmon-index-quant-0.8.1 Page: SAM_to_Sorted_BAM-0.1.9 Page: Samtools 1.7 bamtofastq Page: Samtools 1.7 BAM to SAM Page: Samtools 1.7 flagstat Page: Samtools 1.7 Index BAM file Page: Samtools 1.7 rmdup + flagstat Page: Samtools 1.7 rmdup remove PCR duplicates Page: Samtools 1.7 SAM to BAM format conversion Page: Samtools 1.7 Sort Bam file Page: Samtools 1.7 view - Filter mapped or unmapped reads Page: SAMTools 1.7 mpileup Page: SAMTools 1.7 SAM to sorted BAM Page: SAMTools 1.7 view Filter by region Page: SAMTOOLS-0.1.19 mpileup raw-vcf-out Page: SAMTOOLS-0.1.19 mpileup variant pipeline Page: SAMTOOLS-0.1.19 VCF-Utilities varFilter Page: Samtools_mapping_stats-1.0 Page: Samtools faidx (fasta indexer) Page: SAMtools index BAM file Page: SAMtools view-BEDtools bamtoFastq Page: SAM to sorted BAMv2 Page: Scythe-0.991 using DE Page: Select contigs Page: seqtk_seq-1.0.76 Page: SequenceLogo Page: Sff2Fastq Page: SGA 0.10.15 Pre-Process Reads Page: Sickle-quality-based-trimming version 1.0 Page: SKAT Page: Snap, gene prediction Page: Snap-gene prediction-112913 Page: snp_ase Page: SNP calling illumina seq data Part 2 Page: Soapdenovo Page: Soapdenovo 2.04 Page: Soapdenovo-Trans 1.0 Page: Soapdenovo-trans-small-1.0.4 Page: Sort a File On A Column Page: Sort File On 2 columns Page: SPAdes-3.8.0 Page: Spladder-1.0.0 Page: Split FASTA file Page: SRA-Import-0.1.0 Page: Stampy-build-and-map Page: STAR_2.4.0.1 Page: STAR_2.4.0.1_GenerateGenomeIndex Page: Star-index-align_2.5.3.a Page: StringTie1.3.3 Page: StringTie-1.3.3_merge Page: Structure2Tassel Page: Suffixerator Page: Synapse_client-1.6.1 Page: Syntenic_Feature_Detector Page: taco-0.7.0 Page: Tassel3 Conversion Page: Tassel4 Conversion Page: tbl2asn (gapped)-22.9 using DE Page: tbl2asn (gapped)-25.3 using DE Page: tbl2asn (ungapped)-22.9 using DE Page: tbl2asn (ungapped)-25.3 using DE Page: TIES baseline 1 - averaging Page: TIES baseline 2 - line fitting Page: TIES basic complete run (rev A) Page: TIES step 1 - parse input CSV data Page: TIES step 2 - training full LSS model Page: tophat2gff3 Page: Transcript decoder 1.0 Page: Transcript decoder 2.0 Page: TreeView Page: trim_galore-0.4.1 using DE Page: Trimmomatic-programmable-0.33 Page: Trimmomatic-programmable-0.36 Page: Trinity-64GB-2.1.1 Page: Trinity normalize by k-mer coverage r11.10.13 Page: Trinity r2013-08-14a Page: Trinity r2013-11-10 Page: Tuxedo suite PE up to 4 conditions Page: Uncompress files with gunzip 1.6-2 Page: Uncompress with gunzip Page: Uncompress with tar Page: UNEAK Page: unique filter Page: unpigz-2.3.4 (Uncompress multiple files with ungzip parallely) Page: Validate Page: Variable Region Identifier and Remover Page: Variant annotation using SnpEff in DE Page: VarScan-2.3.6 SNP caller Page: VCF to GFF3 Page: vcfutils.pl varFilter Page: vContact_0.1.49 and vContact-PCs Page: Velvetg-1.2.07 Page: Velvetg-1.2.10 Page: Velvetg-1.2.075 Page: Velvetg-1.2.075-assembly-step2 Page: Velveth-1.2.07 Page: Velveth-1.2.10 Page: Viral Contaimination Detection 1.0 Page: VirSorter 1.0.1 Page: VIRSorter 1.0.2 Page: Weka 3.7.11 Page: Word Count Page: XYPlot 0.0.2