Viewing the User Manual for an App
Click the link to view the app's user manual. (You also can find the manuals for all current apps in the App Info for the app in the DE Apps list.)
To search for an app, enter the app name in the search box below.
- AAARF v 1.0.1
- add column to file
- add column to file2
- Add GO to Blastp-uniprot output
- Admixture
- AgBase GOanna 2.1
- ALLMAPS
- ALLMAPS merge
- ALLMAPS path
- AllpathsLG 44837
- AllpathsLG-small-genomes-44837
- Annotate transcripts
- AntEpiSeeker 2.0
- appendUnclustered
- Assembly Stats (assemblathon tool)
- Assess Assembly vs whole genome
- Bam to Counts (general)
- BAM to Counts (named outputs)
- bayesembler-1.2
- Bayesian BiClustering
- BCFtools 1.8 call
- BCFtools 1.8 index
- BCFtools 1.8 merge VCF
- BCFtools 1.8 view
- BEAST-2.1.3
- BEAST2 on CyVerse UK
- BEAST on CyVerse UK
- BEDTools 2.26.0 bamToBed
- BEDTools 2.26.0 intersectBed
- BEDTools 2.26 fastaFromBed
- BEDTools 2.26 slopBed
- BEDTOOLS BAMtoFastq-2.26
- BEDTools coverageBed
- Bedtools Genome Coverage-BAM-2.26
- BEDTools genomeCoverageBed
- BEDTools maskFastaFromBed
- Best Hit for Blat Output
- Bismark
- Bismark Genome Preparation
- Bismark Methylation Extractor
- Blast2Seqs
- Blastdbcmd-batch-2.6.0
- Blastdbcmd-single-2.6.0
- Blastn-2.2.26
- Blastn-2.6.0+
- Blastp-2.2.29
- Blastp-2.6.0+
- Blastp of a subset of uniprot
- BLASTX (HPC)
- BLAT_psl_to_SAM
- Blat_with_BAM_output
- Blat (default)
- blat 36 (with options)
- Bowtie 1.2.2 build and map
- Bowtie-2.2.1--Build-and-Map
- Bowtie2-2.2.4 Bowtie2-Build indexer and aligner (HPC)
- Bowtie2Build-2.2.4 indexer
- Bowtie-Build
- btrim
- BuildICM-1.0.0-Dev
- Bulk Blast 2 Sequences
- BUSCO in the Discovery Environment
- BUSCO-v2.0 in the Discovery Environment
- BUSCO-v3.0 in the Discovery Environment
- BWA_mem_longreads-0.7.15
- BWA 0.7.12 indexer aligner and mem (HPC)
- BWA 0.7.4 Divergent species
- BWA-0.7.4 non-model species
- BWA Aligner for Paired-End Illumina Reads
- BWA Aligner for Single-End Illumina Reads
- BWA aln 0.7.4
- BWA index 0.7.4
- BWA mem 0.7.15
- bzip2 and bunzip2
- CACE
- Calling SNPs INDELs with SAMtools BCFtools
- Canberra Distance
- Canu 1.7
- CD-HIT-est 4.6.8
- CEGMA
- CharaParser Learn
- CharaParser Markup
- Check covariance matrix file (CheckCvm)
- Check standard GWAS files (CheckGwas)
- Chromatra L
- Chromatra T
- Clean_fasta_header
- ClustalW2
- clusterReport
- CNVnator-0.3.3
- Compress a directory with GNU tar-1.27.1
- Compress files with gzip 1.6-2
- Compress selected files with GNU tar
- Compute Contig Statistics
- Concatenate 2 Files-workflow edition.
- Concatenate Multiple Files
- construction genetic map
- Convert bwt to arf
- Convert SAM-to-sorted-BAM
- ConvertTraitID 0.0.1
- Copy with Scaffolding XML of DESeq2 (multifactorial pairwise comparisons)
- Create_BLAST_database-2.6.0__with_parse_seqids_option
- Create BLAST database
- Create BLAST database-2.6.0+
- create dir
- Cuffcompare-2.2.1
- Cuffdiff
- Cuffdiff2
- CuffDiff 2.2.1a
- Cuffdiff2-16-way-max
- Cuffdiff2 with JS option
- Cufflinks
- Cufflinks_from_SAM-2.2.1 in DE
- Cufflinks 2.2.1
- Cuffmerge2
- Cuffmerge 2.2.1
- curl-7.45.0
- cutadapt
- Cut Columns
- De-interlace paired fasta
- DeltaBLAST-2.2.29+
- de novo population genomics analysis
- DESeq
- DESeq2
- DESeq2 (multifactorial pairwise comparisons)
- DNANJ
- DNAPARS
- dos2unix
- Downsample reads
- draw Venn diagrams
- DREME
- DynamicTrim
- edgeR (multifactorial pairwise comparisons) in DE
- edgeR with Fisher's Exact Test
- EMBOSS Cusp
- EMBOSS Seqret
- Emboss transeq
- Enhanced R Script
- evolinc
- Evolinc_merge-1.0
- Evolinc in the Discovery Environment
- Extract First Lines From a File
- Extract Last Lines From a File
- FALCON (Small Genomes) 0.4.2
- FALCON-formatter
- FASTA Minimum Size Filter
- fastaRename
- FaST-LMM-2.07
- FastLMM Result Plotter
- FaST-LMM Results Plotter 2
- FaST-LMM Reults Plotter 2
- FASTQ_SHRINKER
- FastQC
- FastQC (demo)
- FastQC 0.10.1 (multi-file)
- FastQC-0.11.5 (multi-file)
- fastqCombinePariedEnd
- FastQC-plus 0.10.1 (multi-file)
- Fastq-Join
- Fastq-screen-0.11.1
- Fastq-screen-0.4.4
- FastTree2
- FastTree Dispatcher 2.1.4
- FASTX Barcode Splitter
- FASTX Clipper 0.0.14
- Fastx Collapser
- FASTX fastq quality filter 0.0.14
- FASTX fastq to fasta 0.0.14
- FASTX quality filter and trim
- FASTX Quality Trimmer
- FASTX Toolkit
- FASTX Trimmer 0.0.14
- Filter_CuffDiff_Results
- Filter homozygous SNPs
- filter pileup
- Final filter
- Final filter2
- Find Lines Matching a Regular Expression
- Find SNPS - mpileup
- flattenClusters 1.0
- Freebayes-0.9.20
- GapCloser 1.12
- GATK CombineGCVFs-3.2.2
- GATK GenotypeGVCFs-3.2.2
- GATK HaplotypeCaller
- GATK UnifiedGenotyper-3.2.2
- gbsAlign_BWA 0.5.9
- gbsFilter_TASSEL 3.0.133
- gbsMergeSNP_TASSEL 3.0.133
- gbsTags_TASSEL 3.0.133
- gbsTagsToSNP_TASSEL 3.0.133
- GBS Workflow
- GBS Workflow with user genome
- Generate detectability cartoons for syntenic features
- GeneSeqer_5.0
- GeneSeqer-medium (Stampede) 5.0.0
- Genotype By Sequencing
- Genotyping By Sequencing Workflow
- GenSel
- gffread-2.2.1
- Gfold 1.1.1 Count
- Gfold 1.1.1 Difference Expression
- GLM
- GMAP-7.23.15
- GNU awk
- GNU grep 3.1-2
- GoSeq
- Graphmap index 0.5.2
- Graphmap index align 0.5.2
- Graphmap owler 0.5.2
- GSNAP 07.23.15
- GSNAP 121212
- GWASSER
- Head
- Heterozygote BAM to Counts
- Heterozygote BAM to Counts, v1.2
- Hisat2-Cuffcompare v1.0
- HISAT2-index-align
- HTProcess_BAMstats-1.0
- HTProcess_CuffDiff-2.2.0
- HTProcess_Cufflinks-2.2.0
- HTProcess_Cufflinks-2.2.1
- HTProcess_Cuffmerge-1
- HTProcess_Cuffmerge-2.2.1
- HTProcess_fastqc-0.1
- HTProcess_fastqc-0.2
- HTProcess_Jellyfish-2.0.0
- HTProcess_Kmergenie-1.0
- HTProcess_Kmergenie-1.7016
- HTProcess_Tophat-2.0.11 (archived)
- HTProcess_Tophat 2.0.13 (archived)
- HTProcess_trimmomatic_0.32
- HTProcess_trimmomatic-0.33
- HTProcess-prepare_directories-and-run_fastqc-0.1
- HTProcess-prepare input directories-0.1
- HTProcess-prepare input directories 0.2
- HTProcess-Tophat-2.0.11 (archived)
- HTProcess-Tophat-2.1.1 (archived)
- HTSeq-count 0.5.4
- HTSeq-count-0.6.1
- HTSeq-with-BAM-input
- IDBA-UD 1.1.2
- Identification of unique homozygous SNPs in mutant
- IGVtools count
- Index BAM file
- Index BAM--get stats
- Index fasta file (Samtools 1.7 faidx)
- InStruct
- Interlace Paired FASTQ files
- InterProScan_Results_Function
- InterproScan 5.17.56
- IUTA-1.0 in the Discovery Environment
- Join multiple tab-delimited files
- Kallisto
- KBase data upload
- khmer 3.0.0a1 extract paired reads
- khmer 3.0.0a1 filter-abund
- khmer 3.0.0a1 load into counting
- khmer 3.0.0a1 normalize by median
- LASTAL-8.69
- LASTDB-8.69
- LD (Tassel4)
- Linux stream editor
- List contents of FAST5 file(s)
- MACS
- MAFFT 7.0.17
- Make new names for fasta sequences
- maker2jbrowse
- maker2zff
- Mapping illumina seq data Part 1
- MaxBin 2.2 in the Discovery Environment
- Medusa-1.6
- Megahit-1.0.6
- Merge_htseq_count-1.0
- Merge BAM files
- MergeG2P 0.0.2
- Merge SFF files-2.9
- MERRA-AS instM_3d_ana_Np (Analyzed State, Meteorology Instantaneous Monthly)
- MERRA-AS tavg1_2d_lnd_Nx (Land related surface quantities)
- MetaGeneAnnotator-1.0.0
- MetaGeneMark GFF to IGB
- MetaPhyler-SR 0.115
- MetaQUAST-4.0 (denovo based) in DE
- MetaQUAST-4.0 (reference based) in DE
- MetaQUAST-4.3 (denovo based) in DE
- MetaQUAST-4.3 (reference based) in DE
- Mikado
- Miniasm 0.2_r168
- Minimap2_index_align-2.10
- Minimap2_index-2.10
- miRanda 3.3a
- miRDeep2 2.0.0.8
- miRDeep2 2.0.0.8 mapper
- miRDeep2 2.0.0.8 quantifier
- MLM (Tassel4)
- MLM 4.3.13
- MLMM 0.0.2
- MLM Workflow
- Modify_GFF_coordinates
- Molecular Dating with Penalized Likelihood
- mpileup
- MrBayes_mpi_basic-3.2.3
- MrBayes on CyVerse UK
- MUSCLE
- MUSCLE-3.8.31 on Stampede
- Mutant Identification 1
- mutant interval identification
- Nanopolish-call-methylation-0.10.2
- Nanopolish-eventalign-0.10.2
- Nanopolish-eventalign-0.7.1
- Nanopolish-extract-0.10.2
- Nanopolish-extract-0.8.1
- Nanopolish-index-0.10.2
- Nanopolish-index-0.8.1
- Nanopolish-variants-0.10.2
- Nanopolish vcf2fasta 0.10.2
- NCBI GenBank Import
- NCBI SRA Import
- NCBI SRA Import 1.2
- NCBI SRA Submission - BioProject Creation
- NCBI SRA Submission - BioProject Update
- NCBI SRA Submission Report Retrieval
- NCBI SRA Toolkit fastq-dump 2.1.9
- NCBI SRA Toolkit fastq-dump 2.3.4
- NCBI SRA Toolkit fastq-dump 2.8.1
- NCBI SRA to Solid Format (abi-dump)
- Newbler
- Newbler 2.6.0
- Ninja
- non-unique filter
- Normalize By Median
- NPUTE-0.0.1
- NumericalTransform 4.3.14
- Numeric Evaluation of a Data Column
- Oases 0.2.08
- Ontologizer
- OposSOM-2.0.1-biomart
- OrthoMCL v1.4
- PAGE
- PAML
- ParaAT 2.0
- parallel-fastq-dump-0.6.1
- parseBlastBpo
- Parse Blast Report
- Parser-3.0.20
- PcPipe 1.0.0
- Peak Ranger
- Peak Ranger_ranger_1.18
- Peak Ranger_wig_1.18
- Peak Ranger_wigpe_1.18
- PEAR-0.9.6
- PepMOD
- PGDSpider tool for data conversion
- Photometry-pipeline-v1.0
- PhyML
- Picard-MarkDuplicates-2.7.1 in the Discovery Environment
- Picard Preprocess-1.98
- pigz-2.3.4 (Compress multiple files with gzip parallely)
- PK Unzip
- Platypus-0.7.9.5
- PLINK
- PLINK 1.90b4
- PLINK 1.90b4 Conversion
- PLINK 2 AntEpiSeeker Conversion
- PLINK Conversion
- Polymarker
- population genomics analysis flow
- Principal Component Analysis
- Prinseq-Graph-noPCA evaluate reads
- Prinseq-lite
- Prodigal
- ProgressiveMauve
- PROML
- PROTNJ
- PROTPARS
- QIIME-1.9.1 in Discovery Environment
- QTL Cartographer
- QTL simulation workflow
- QUAST (3.2 and 4.0) in the Discovery Environment
- queryOrthoMCL 1.0
- Rascaf V1.0.2 in Discovery Environment
- RAxML-7.3.0
- RAxML-8.2.3_small_and_medium
- RAxML on CyVerse UK
- raxml-RFdistance-8.2.11
- Ray-2.3.1
- Rename contigs 2.0
- rePair-Fix Read Pairing
- rnaQUAST_1.2.0 (de novo based)
- rnaQUAST 1.2.0 (reference based) using DE
- RSEM 1.2.12
- RSEM-Prepare-Reference 1.2.19
- Sabre-barcode-demultiplexing
- Sailfish_align_quant-0.9.2
- salmon-index-quant-0.8.1
- SAM_to_Sorted_BAM-0.1.9
- Samtools_mapping_stats-1.0
- SAMTOOLS-0.1.19 mpileup raw-vcf-out
- SAMTOOLS-0.1.19 mpileup variant pipeline
- SAMTOOLS-0.1.19 VCF-Utilities varFilter
- Samtools 1.7 bamtofastq
- Samtools 1.7 BAM to SAM
- Samtools 1.7 flagstat
- Samtools 1.7 Index BAM file
- SAMTools 1.7 mpileup
- Samtools 1.7 rmdup + flagstat
- Samtools 1.7 rmdup remove PCR duplicates
- Samtools 1.7 SAM to BAM format conversion
- SAMTools 1.7 SAM to sorted BAM
- Samtools 1.7 Sort Bam file
- SAMTools 1.7 view Filter by region
- Samtools 1.7 view - Filter mapped or unmapped reads
- Samtools faidx (fasta indexer)
- SAMtools index BAM file
- SAMtools view-BEDtools bamtoFastq
- SAM to sorted BAMv2
- Scythe-0.991 using DE
- Select contigs
- seqtk_seq-1.0.76
- SequenceLogo
- Sff2Fastq
- SGA 0.10.15 Pre-Process Reads
- Sickle-quality-based-trimming version 1.0
- SKAT
- Snap, gene prediction
- Snap-gene prediction-112913
- snp_ase
- SNP calling illumina seq data Part 2
- Soapdenovo
- Soapdenovo 2.04
- Soapdenovo-Trans 1.0
- Soapdenovo-trans-small-1.0.4
- Sort a File On A Column
- Sort File On 2 columns
- SPAdes-3.8.0
- Spladder-1.0.0
- Split FASTA file
- SRA-Import-0.1.0
- Stampy-build-and-map
- STAR_2.4.0.1
- STAR_2.4.0.1_GenerateGenomeIndex
- Star-index-align_2.5.3.a
- StringTie1.3.3
- StringTie-1.3.3_merge
- Structure2Tassel
- Suffixerator
- Synapse_client-1.6.1
- Syntenic_Feature_Detector
- taco-0.7.0
- Tassel3 Conversion
- Tassel4 Conversion
- tbl2asn (gapped)-22.9 using DE
- tbl2asn (gapped)-25.3 using DE
- tbl2asn (ungapped)-22.9 using DE
- tbl2asn (ungapped)-25.3 using DE
- TIES baseline 1 - averaging
- TIES baseline 2 - line fitting
- TIES basic complete run (rev A)
- TIES step 1 - parse input CSV data
- TIES step 2 - training full LSS model
- tophat2gff3
- Transcript decoder 1.0
- Transcript decoder 2.0
- TreeView
- trim_galore-0.4.1 using DE
- Trimmomatic-programmable-0.33
- Trimmomatic-programmable-0.36
- Trinity-64GB-2.1.1
- Trinity normalize by k-mer coverage r11.10.13
- Trinity r2013-08-14a
- Trinity r2013-11-10
- Tuxedo suite PE up to 4 conditions
- Uncompress files with gunzip 1.6-2
- Uncompress with gunzip
- Uncompress with tar
- UNEAK
- unique filter
- unpigz-2.3.4 (Uncompress multiple files with ungzip parallely)
- Validate
- Variable Region Identifier and Remover
- Variant annotation using SnpEff in DE
- VarScan-2.3.6 SNP caller
- VCF to GFF3
- vcfutils.pl varFilter
- vContact_0.1.49 and vContact-PCs
- Velvetg-1.2.07
- Velvetg-1.2.075
- Velvetg-1.2.075-assembly-step2
- Velvetg-1.2.10
- Velveth-1.2.07
- Velveth-1.2.10
- Viral Contaimination Detection 1.0
- VirSorter 1.0.1
- VIRSorter 1.0.2
- Weka 3.7.11
- Word Count
- XYPlot 0.0.2
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: Graphmap index 0.5.2
Page: Graphmap index align 0.5.2
Page: Graphmap owler 0.5.2
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: List contents of FAST5 file(s)
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: OposSOM-2.0.1-biomart
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