AtacENCODEApp
ATAC A ATAC-seq and DNase-seq processing pipeline from ENCODE.
Name, Read1, Read2, Species
Name, Report [File], Stats [File], Html [Link]
HomerDiffPeaksApp
ATAC Finding Peaks and Differential Peaks with or without Replicates from HOMER.
Name, BAM
Name, Report [File], DiffPeak [Link]
ProdigalApp
Annotate Prodigal: rapid prokaryotic genome annotation
Name, Draft
Name, Out [File], Proteins [File], Species
ProkkaApp
Annotate Prokka: rapid prokaryotic genome annotation
Name, Draft
Name, ProkkaOut [File], Species
PsortbApp
Annotate Psortb: subcellular protein localization prediction tool for Bacteria and Archea
Name, Proteins
Name, PsortbOut [File], Species
CanuApp
Assemble Canu long read genome assembler
Name, Read1
Name, Reads, Draft [File]
SpadesApp
Assemble SPAdes genome assembler
Name, Read1
Name, Draft [File], SpadesLog [File], PreprocessingLog [File], Species, Read Count
UnicyclerApp
Assemble Unicycler microbial genome assembler
Name, Read1
Name, Draft [File], Graph [File], Log [File], Species, Read Count
ExceRptApp
Count Annotation and Profiling of smallRNA-seq with exceRpt's pipeline
Name, Read1, Adapter1, Species
Name, excerpt [File], Species, refBuild
FeatureCountsApp
Count Multi-purpose read counting with Rsubread::featureCounts
Name, BAM, BAI, refBuild
Name, Count [File], Stats [File], Species, refBuild, featureLevel, refFeatureFile, strandMode, paired, Read Count, transcriptTypes
KallistoApp
Count kallisto is a program for quantifying abundances of transcripts from RNA-Seq data. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
Name, Read1, Species
Name, Count [File], bootstrappedCount [File], runInfo [File], PreprocessingLog [File], Species, refBuild, featureLevel, refFeatureFile, strandMode, paired, Read Count, transcriptTypes
DESeq2App
Differential_Expression Differential gene expression analysis based on the negative binomial distribution
Name, Count, Species, refBuild, featureLevel, refFeatureFile
Name, Species, refBuild, Static Report [Link], Live Report [Link], Report [File]
EdgeRApp
Differential_Expression Empirical analysis of digital gene expression data in R
Name, Count, Species, refBuild, featureLevel, refFeatureFile
Name, Species, refBuild, Static Report [Link], Live Report [Link], Report [File]
LimmaApp
Differential_Expression Empirical analysis of digital gene expression data in R
Name, Count, Species, refBuild, featureLevel, refFeatureFile
Name, Species, refBuild, Static Report [Link], Live Report [Link], Report [File]
BWAApp
Map Burrows-Wheeler Aligner
Name, Read1, Species
Name, BAM [File], BAI [File], IGV [Link], Species, refBuild, paired, refFeatureFile, strandMode, Read Count, IGV [File], PreprocessingLog [File]
BismarkApp
Map A tool to map bisulfite converted sequence reads and determine cytosine methylation states
Name, Read1, Species
Name, BAM [File], BAI [File], TxtReport [File], M-Bias_R1 [File], M-Bias_R2 [File], CpG_Context [File], COV [File], BedGraph [File], Species, refBuild, paired, Read Count, PreprocessingLog [File]
Bowtie2App
Map Fast and sensitive read alignment. Supports local and end-to-end mode
Name, Read1, Species
Name, BAM [File], BAI [File], IGV [Link], Species, refBuild, paired, Read Count, IGV [File], PreprocessingLog [File], Bowtie2Log [File]
Minimap2App
Map https://lh3.github.io/minimap2/minimap2.html
Name, Read1, Species
Name, BAM [File], BAI [File], IGV [Link], Species, refBuild, paired, refFeatureFile, strandMode, Read Count, IGV [File], PreprocessingLog [File]
Pbmm2App
Map A minimap2 frontend for PacBio native data formats
Name, Read1
Name, BAM [File], BAI [File], IGV [Link], refBuild, IGV [File], Pbmm2Log [File]
STARApp
Map Ultafast spliced alignment
Name, Read1, Species
Name, BAM [File], BAI [File], IGV [Link], Species, refBuild, paired, refFeatureFile, strandMode, Read Count, IGV [File], PreprocessingLog [File], STARLog [File]
KrakenApp
Metagenomics Kraken taxonomic sequence classification system
Name, Read1
Name, KronaReport [Link], KrakenOut [File], KrakenReport [File], KronaOutDir [File], KronaOut [File]
PostSamsa2AnalysisApp
Metagenomics Step_6 of Samsa2, data analysis and report.
Name, annotationORGFileRefSeq, annotationFUNCFileRefSeq
Name, Report [File], Static Report [Link]
QIIME2App
Metagenomics Data processing with QIIME2. For short reads/Illumina data only.
Name, Read1
Name, ResultDir [File], Static Report [Link], Demux Report [Link], Denoising stats [Link], Feature Table [Link], Rep Seqs Report [Link], Taxonomy Barplot [Link], Taxonomy List [Link], Shannon Diversity [Link], Jaccard Diversity [Link], Bray Curtis Diversity [Link], Jaccard Emperor Plot [Link], Bray Curtis Emperor Plot [Link], Alpha rarefaction [Link], Differential abundace [Link]
Samsa2App
Metagenomics Metatranscriptomics pipeline with Samsa2.
Name, Read1
Name, annotationFileRefSeq [File], annotationORGFileRefSeq [File], annotationFUNCFileRefSeq [File]
VirDetectApp
Metagenomics Virome analysis for the diagnostic use in veterinary virology
Name, Read1, Species
Name, Species, virBuild, hostBuild, paired, Read Count, OutDir [File], OutReport [Link]
CountSpacerApp
Misc QC Tool for sgRNA libraries.
Name, Read1
Name, Report [File], Html [Link], Count [File], Species, Read Count
MageckCountApp
Misc
Name, Read1
Name, Count [File], Log [File], Read Count, libName, Species
NestLinkApp
Misc NestLink - an R data package to guide through Engineered Peptide Barcodes for In-Depth Analyzes of Binding Protein Ensembles - https://bioconductor.org/packages/release/data/experiment/html/NestLink.html
Name, Read1, FlashLog
Name, NestLink Result [File]
MACS2App
Peaks Capturing the influence of genome complexity to evaluate the significance of enriched ChIP regions
Name, BAM, BAI, refBuild
Name, Species, refBuild, refFeatureFile, paired, CalledPeaks [File], BED [File], PeakSequences [File], BigWigFile [File], BAM [File], BAI [File]
ConvERDSApp
Polyploid This converts the result DataSet of EAGLERCApp to an input DataSet of DNAHaplotypeCallerGVCFApp.
Name, Species, dummy
Name, BAM, refBuild, Species, Dummy [File]
EAGLERCApp
Polyploid EAGLE: Explicit Alternative Genome Likelihood Evaluator
Name, BAM1, BAM2, refBuild1, refBuild2, Species
Name, Parent1RefBAM [File], Parent1AltBAM [File], Parent1UnkBAM [File], Parent1MulBAM [File], refBuild1, Parent2RefBAM [File], Parent2AltBAM [File], Parent2UnkBAM [File], Parent2MulBAM [File], stdout log [File], errout log [File], refBuild2, Species, dummy [File]
MergeDataSetApp
Polyploid Merging two DataSets
Name, BAM, refBuild, Species
Name, BAM1, BAM2, refBuild1, refBuild2, Species, dummy [File]
FlashApp
Prep Fast Length Adjustment of SHort reads
Name, Read1, Read2
Name, Read1 [File], Log [File], Species, Read Count
MergeRunDataApp
Prep Merging fastq files from two illumina runs by name
Name, Species, Read1
Name, Result [File]
EnaApp
PublicData Download public data from ENA
Name, projectID
Name, projectID, ENA Result [File]
BuscoApp
QC BUSCO: from QC to gene prediction and phylogenomics
Name, Draft
Name, BuscoPlot [Link], BuscoOut [File], Species
CountQCApp
QC Quality control after counting reads
Name, Count, Species, refBuild, featureLevel, refFeatureFile
Name, Species, refBuild, Static Report [Link], Live Report [Link], Report [File]
CrisprScreenQCApp
QC Screens of CRISPR samples for contaminations
Name, Read1
Name, Report [File], Html [Link]
DnaBamStatsApp
QC Runs the following tools that check alignment statistics for the DNA applications
Name, BAM
Name, Samstat Result [File], Qualimap Result [File], Picard Result [File], Samstat Report [Link], Qualimap Report [Link], Picard Report [Link]
DnaQCApp
QC Quality control after the alignment of RNAseq reads
Name, BAM, BAI, refBuild, Species
Name, Report [File], Html [Link], Species, refBuild, refFeatureFile
ExceRptReportApp
QC QC report of exceRpt outputs.
Name, excerpt, Species, refBuild
Name, Species, refBuild, Static Report [Link], Report [File]
ExploreMageckCountsApp
QC Quality control after counting sgRNAs with Mageck
Name, Count, Species
Name, Species, libName, Static Report [Link], Live Report [Link], Report [File]
FastqScreen10xApp
QC Screen files for contaminations or ribosomal RNA content
Name, RawDataDir, Read Count
Name, Report [File], Html [Link]
FastqScreenApp
QC Screen files for contaminations or ribosomal RNA content
Name, Read1, Read Count
Name, Report [File], Html [Link]
Fastqc10xApp
QC A quality control tool for NGS reads
Name, RawDataDir, Read Count
Name, Report [File], Html [Link], MultiQC [Link]
FastqcApp
QC A quality control tool for NGS reads
Name, Read1
Name, MultiQC Report [Link], MultiQC [File], FastQC [File]
GceApp
QC GCE(genomic charactor estimator): a bayes model based method to estimate the genome size, genomic repeat content and the heterozygsis rate of the sequencing sample
Name, Read1
Name, GCE Result [File], Report [Link]
MageckTestApp
QC Run test module in the tool Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK )
Name, Count
Name, Report [File], Report [Link]
NanoPlotApp
QC NanoPlot: Plotting tool for long read sequencing data and alignments
Name, Read1
Name, NanoPlot Result [File], Report [Link]
PreqcApp
QC Preqc - Illumina read pre-assembly quality control and data exploration module within sga
Name, Read1, Read2
Name, PreqcReport [Link], PreqcReport [File], PreqcOut [File]
QuastApp
QC QUAST (Quality Assessment Tool for Genome Assemblies)
Name, Draft
Name, QuastReport [Link], QuastOut [File], Species
RnaBamStatsApp
QC Quality control after the alignment of RNAseq reads
Name, BAM, BAI, refBuild, Species
Name, Report [File], Html [Link], Species, refBuild, refFeatureFile
RnaBiasApp
QC Name, Read1, Species
Name, Report [File], Report [Link]
BDRhapsodySAApp
SingleCell This wrapper runs a CWL workflow for the analysis of BD Single-Cell Multiomics.
Name, Read1, Read2, Species
Name, Species, refBuild, refFeatureFile, featureLevel, transcriptTypes, SCDataOrigin, ResultDir [File], Report [Link], CountMatrix [Link], UnfilteredCountMatrix [Link], Read Count
CellBenderApp
SingleCell CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data. ToolLink: https://github.com/broadinstitute/CellBender
Name, Species, refBuild, refFeatureFile, CountMatrix
Name, Species, refBuild, refFeatureFile, Static Report [Link], ResultDir [File], CountMatrix [Link], UnfilteredCountMatrix [Link]
CellRangerARCApp
SingleCell This wrapper runs cellranger-arc count in Single-library analysis mode.
Name, RNADataDir, ATACDataDir, Species
Name, Species, refBuild, refFeatureFile, featureLevel, ResultDir [File], Report [Link], CountMatrix [Link], UnfilteredCountMatrix [Link], Read Count
CellRangerATACApp
SingleCell This wrapper runs cellranger atac count in Single-library analysis mode.
Name, RawDataDir, Species
Name, Species, refBuild, refFeatureFile, featureLevel, ResultDir [File], Report [Link], CountMatrix [Link]
CellRangerAggrApp
SingleCell This wrapper runs cellranger aggr in multi-library analysis mode.
Name, CountMatrix
Name, Species, refBuild, refFeatureFile, featureLevel, transcriptTypes, ResultDir [File], Report [Link], CountMatrix [Link]
CellRangerApp
SingleCell This wrapper runs cellranger count in Single-library analysis mode.
Name, RawDataDir, Species
Name, Species, refBuild, refFeatureFile, featureLevel, transcriptTypes, SCDataOrigin, ResultDir [File], Report [Link], CountMatrix [Link], UnfilteredCountMatrix [Link], Read Count
CellRangerMultiApp
SingleCell This wrapper runs cellranger multi in Single-library analysis mode.
Name, RawDataDir, Species
Name, Species, refBuild, refFeatureFile, featureLevel, transcriptTypes, SCDataOrigin, ResultDir [File,Link], Read Count
MergeSCDataSetsApp
SingleCell Merging more than two DataSets generaged from same library for CellRangerApp
Name, Species, RawDataDir
Name, Species
ONTwfScApp
SingleCell A research pipeline designed to identify the cell barcode and UMI sequences present in nanopore sequencing reads generated from single-cell gene expression libraries
Name, Read1
Name, OutDir [File], OutReport [Link]
SCFeatBarcodingApp
SingleCell Single cell report
Name, Species, refBuild, CountMatrix, ResultDir
Name, Species, refBuild, refFeatureFile, Static Report [Link], Report [File]
SCTrajectoryInferenceApp
SingleCell Trajectory inference analysis for single cell data
Name, Static Report
Name, Report [File], Static Report [Link]
STARsoloApp
SingleCell This wrapper runs STARsolo in Single-library analysis mode. Note that it only runs on Single Cell GEX 10X libraries.
Name, RawDataDir, Species
Name, Species, refBuild, refFeatureFile, featureLevel, soloFeatures, transcriptTypes, ResultDir [File], CountMatrix [Link], UnfilteredCountMatrix [Link]
ScSeuratApp
SingleCell Single cell report
Name, Species, refBuild, CountMatrix, ResultDir, Condition
Name, Species, refBuild, refFeatureFile, Static Report [Link], SC Cluster Report [File], SC Seurat
ScSeuratCombineApp
SingleCell The report of merged single cell samples/plates
Name, Species, refBuild, refFeatureFile, Static Report
Name, Species, Static Report [Link], Report [File]
ScSeuratCombinedLabelClusters
SingleCell The report of merged single cell samples/plates
Name, Species, Static Report, Report
Name, Species, Static Report [Link], Report [File]
ScSeuratCompareApp
SingleCell Empirical analysis of digital gene expression data in R
Name, Report
Name, Static Report [Link], Report [File]
ScSeuratFilterClustersApp
SingleCell Single cell report
Name, Species, refBuild, SC Seurat
Name, Species, refBuild, refFeatureFile, Static Report [Link], SC Cluster Report [File], SC Seurat
ScSeuratLabelClustersApp
SingleCell Single cell report
Name, Species, refBuild, SC Seurat
Name, Species, refBuild, refFeatureFile, Static Report [Link], SC Cluster Report [File], SC Seurat
VelocytoApp
SingleCell This wrapper runs velocyto in Single-library analysis mode.
Name, ResultDir
Name, LOOM [File], Species, refBuild, refFeatureFile, featureLevel, Read Count
SpaceRangerAggrApp
Spatial This wrapper runs spaceranger aggr in multi-library analysis mode.
Name, CountMatrix
Name, Species, refBuild, refFeatureFile, featureLevel, transcriptTypes, ResultDir [File], Report [Link], CountMatrix [Link]
SpaceRangerApp
Spatial This wrapper runs space ranger count in Single-library analysis mode.
Name, RawDataDir, Species, Slide, Area
Name, Species, refBuild, refFeatureFile, featureLevel, transcriptTypes, ResultDir [File], Report [Link], CountMatrix [Link], Read Count, Count [Link]
SpatialSeuratApp
Spatial Single cell report
Name, Species, refBuild, CountMatrix, ResultDir
Name, Species, refBuild, refFeatureFile, Static Report [Link], Report [File]
SpatialSeuratSlidesApp
Spatial Combine multiple slides from Visium/plates
Name, Species, refBuild, refFeatureFile, Static Report
Name, Species, Static Report [Link], Report [File]
WordCountApp
Stats test applicaiton Supercalifragilisticexpialidocious!!
Name, Read1
Name, Stats [File], Options
GATKJointGenotypingByGenomicsDBApp
Variants Genotyping by GenomicsDBImport,GenotypeGVCFs, and hard-filtering by VariantFiltration
Name, GVCF, GVCFINDEX, Species, refBuild, Dummy
Name, Raw VCF [File], Filtered VCF [File], Species, refBuild
GATKv4DNAHaplotypeCallerGVCFApp
Variants Haplotype calling for DNA-seq with > version 4.0 in GVCF mode
Name, BAM, refBuild, Dummy
Name, GVCF [File], GVCFINDEX [File], Species, refBuild, Dummy [File]
GATKv4FilteringSNPsByReferenceVCFApp
Variants filtering out SNPs by the VCF coming from reference accession
Name, Raw VCF, Filtered VCF, Species, refBuild
Name, Filtered VCF [File], Species, refBuild, Script [File], Script log [File]
GATKv4GVCF2FilteredVCFApp
Variants genotype,merge and annotate gvcf-Files
Name, GVCF, GVCFINDEX, Species, refBuild, Dummy
Name, Raw VCF [File], Filtered VCF [File], Species, refBuild
GATKv4JointGenoTypesApp
Variants genotype,merge and annotate gvcf-Files
Name, GVCF, GVCFINDEX, Species, refBuild, Dummy
Name, Raw VCF [File], Filtered VCF [File], Species, refBuild
GatkDnaHaplotyperApp
Variants Haplotype calling for DNA-seq
Name, BAM, BAI, refBuild
Name, GVCF [File], GVCFINDEX [File], Species, targetFile, refBuild
GatkJoinGenoTypesApp
Variants genotype,merge and annotate gvcf-Files
Name, GVCF, GVCFINDEX, Species, refBuild
Name, Report [File], Species, refBuild
GatkRnaHaplotyperApp
Variants Haplotype calling for RNA-seq
Name, BAM, BAI, refBuild
Name, GVCF [File], GVCFINDEX [File], Species, refBuild
MpileupApp
Variants Variant analysis with samtools/bcftools.
Name, BAM, BAI, refBuild, Species
Name, VCF [File], TBI [File], Report [File], Html [Link], Species, refBuild
PbsvApp
Variants pbsv - PacBio structural variant (SV) calling and analysis tools
Name, BAM, BAI, refBuild
Name, refBuild, OutDir [File], OutReport [Link]
