List of Applications
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.)
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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-1.13 VCF-Utilities varFilter
- BCFtools 1.8 call
- BCFtools 1.8 index
- BCFtools 1.8 merge VCF
- BCFtools 1.8 query
- BCFtools 1.8 view
- BEAST-2.1.3
- BEAST 2.6.3
- 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
- bgzip
- 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)
- chloroExtractor 1.0.9
- 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)
- DIAMOND 0.9.10
- DIAMOND-makedb-0.9.10
- 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 cpgplot
- EMBOSS Cusp
- EMBOSS Seqret
- Emboss transeq
- Enhanced R Script
- evolinc
- Evolinc_merge-1.0
- Evolinc in the Discovery Environment
- Exonerate 2.2.0
- 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
- Fastp 0.20.1
- 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-multx-1.4.0
- 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
- Fluorescent Imaging Pipeline (FLIP)
- 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
- gffread-2.2.1 convert between GFF3 and GTF2
- Gfold 1.1.1 Count
- Gfold 1.1.1 Difference Expression
- GLM
- gmap_build-2018-03-25
- gmap-2018-03-25
- 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-0.12.4
- HTSeq-count 0.5.4
- HTSeq-count-0.6.1
- Htseq-Count-Merge-0.6.1
- HTSeqQC
- 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 5.36.75
- 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
- LTR finder 1.07
- 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
- miR-PREFeR
- 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
- Mugsy 1.2.3
- 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
- NGMLR 0.2.7
- 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
- OrthoFinder 2.5.2
- 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 2.1.1.5
- 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
- POLCA 3.4.2
- 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
- Repliscan
- RMTA v2.6.3
- rnaQUAST_1.2.0 (de novo based)
- rnaQUAST 1.2.0 (reference based) using DE
- rRNAFilter 1.1
- RSEM 1.2.12
- RSEM-Prepare-Reference 1.2.19
- RseqFilt-1.0
- rust-mdbg 0.1.0
- rust-mdbg 0.1.0 magic-simplify
- rust-mdbg 0.1.0 multik
- rust-mdbg 0.1.0 pipeline
- 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 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
- SNPhylo
- 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
- Stacks 2.53 populations
- 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
- Structure 2.3.4
- Structure2Tassel
- Suffixerator
- Synapse_client-1.6.1
- Syntenic_Feature_Detector
- tabix 0.2.6
- taco-0.7.0
- Tassel3 Conversion
- Tassel4 Conversion
- tbl2asn (gapped)-22.9 using DE
- tbl2asn (gapped)-25.8 using DE
- tbl2asn (ungapped)-22.9 using DE
- tbl2asn (ungapped)-25.8 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
- TPM calculator 0.0.3
- 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
- vcf2phylip
- VCF to GFF3
- vcftools-compare 0.1.16
- vcftools-concat 0.1.16
- vcftools-merge 0.1.16
- vcftools-phased-join 0.1.16
- vcftools-stats 0.1.16
- 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-1.2.0
- Viral Contaimination Detection 1.0
- VirSorter 1.0.1
- VIRSorter 1.0.2
- Weka 3.7.11
- WGCNA
- Word Count
- wtdbg 2.3
- wtpoa-cns 2.3
- XYPlot 0.0.2