Viewing the User Manual for an App
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- 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
- Ballgown-2.0
- 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 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 1.8
- 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
- clusterProfiler
- clusterReport
- CNVnator-0.3.3
- combine GAFs
- 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
- DataHog
- 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 5.0.5
- 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-Sample-0.8
- 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
- File_Select v1.0
- File_Split v1.0
- 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
- GOanna
- 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-Count-Merge-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)
- Infernal-1.1.2
- 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
- KOBAS annotate 3.0.3
- KOBAS annotate and identify 3.0.3
- KOBAS identify 3.0.3
- LASTAL-8.69
- LASTDB-8.69
- LD (Tassel4)
- Linux stream editor
- List contents of FAST5 file(s)
- LncTar-1.0
- 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
- Meraculous 2.2.6
- 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
- nanofilt 2.5.0
- 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
- nanoqc 0.91
- 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
- parallel-fastq-dump-multi-0.6.5
- 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
- Porechop 0.2.3
- Poretools combine 0.6.1a1
- Poretools events 0.6.1a1
- Poretools fasta 0.6.1a1
- Poretools fastq 0.6.1a1
- Poretools index 0.6.1a1
- Poretools metadata 0.6.1a1
- Poretools nucdist 0.6.1a1
- Poretools qualdist 0.6.1a1
- Poretools readstats 0.6.1a1
- Poretools stats 0.6.1a1
- Poretools times 0.6.1a1
- Poretools winner 0.6.1a1
- 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
- RMTA v2.6.1
- 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
- RseqFilt-1.0
- 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
- Scrappie
- Scythe-0.991 using DE
- Select contigs
- seqtk_seq-1.0.76
- SequenceLogo
- Seurat VICE app in DE
- Sff2Fastq
- SGA 0.10.15 Pre-Process Reads
- Sickle-quality-based-trimming version 1.0
- SKAT
- Sleuth
- Snap, gene prediction
- SnapATAC VICE app in DE
- 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
- Sspace
- 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
- TransDecoder 5.5.0
- TransDecoder 5.5.0 detect coding regions
- TransDecoder 5.5.0 extract long ORFs
- TreeView
- trim_galore-0.4.1 using DE
- Trimmomatic-programmable-0.33
- Trimmomatic-programmable-0.36
- Trimmomatic-programmable-0.38
- 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
- VIBRANT-1.0.1
- Viral Contaimination Detection 1.0
- VirSorter 1.0.1
- VIRSorter 1.0.2
- Weka 3.7.11
- Word Count
- wtdbg 2.3
- wtpoa-cns 2.3
- 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: Ballgown-2.0
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 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 1.8
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: clusterProfiler
Page: clusterReport
Page: CNVnator-0.3.3
Page: combine GAFs
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: DataHog
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 5.0.5
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-Sample-0.8
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: File_Select v1.0
Page: File_Split v1.0
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: GOanna
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-Count-Merge-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: Infernal-1.1.2
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: KOBAS annotate 3.0.3
Page: KOBAS annotate and identify 3.0.3
Page: KOBAS identify 3.0.3
Page: LASTAL-8.69
Page: LASTDB-8.69
Page: LD (Tassel4)
Page: Linux stream editor
Page: List contents of FAST5 file(s)
Page: LncTar-1.0
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: Meraculous 2.2.6
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: nanofilt 2.5.0
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: nanoqc 0.91
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: parallel-fastq-dump-multi-0.6.5
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: Porechop 0.2.3
Page: Poretools combine 0.6.1a1
Page: Poretools events 0.6.1a1
Page: Poretools fasta 0.6.1a1
Page: Poretools fastq 0.6.1a1
Page: Poretools index 0.6.1a1
Page: Poretools metadata 0.6.1a1
Page: Poretools nucdist 0.6.1a1
Page: Poretools qualdist 0.6.1a1
Page: Poretools readstats 0.6.1a1
Page: Poretools stats 0.6.1a1
Page: Poretools times 0.6.1a1
Page: Poretools winner 0.6.1a1
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: RMTA v2.6.1
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: RseqFilt-1.0
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: Scrappie
Page: Scythe-0.991 using DE
Page: Select contigs
Page: seqtk_seq-1.0.76
Page: SequenceLogo
Page: Seurat VICE app in DE
Page: Sff2Fastq
Page: SGA 0.10.15 Pre-Process Reads
Page: Sickle-quality-based-trimming version 1.0
Page: SKAT
Page: Sleuth
Page: Snap, gene prediction
Page: SnapATAC VICE app in DE
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: Sspace
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: TransDecoder 5.5.0
Page: TransDecoder 5.5.0 detect coding regions
Page: TransDecoder 5.5.0 extract long ORFs
Page: TreeView
Page: trim_galore-0.4.1 using DE
Page: Trimmomatic-programmable-0.33
Page: Trimmomatic-programmable-0.36
Page: Trimmomatic-programmable-0.38
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: VIBRANT-1.0.1
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: wtdbg 2.3
Page: wtpoa-cns 2.3
Page: XYPlot 0.0.2