HomerDiffPeaksApp
ATAC Finding Peaks and Differential Peaks with or without Replicates from HOMER.
Name, BAM
Name, Report [File], DiffPeak [Link]
NfCoreAtacSeqApp
ATAC A ATAC-seq processing pipeline from NF-Core.
Name, Read1, Read2, Species
Name, Species, refBuild, grouping, Result [File], Report [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, Proteins [File], ProkkaOut [File], Species
PsortbApp
Annotate Psortb: subcellular protein localization prediction tool for Bacteria and Archea
Name, Proteins
Name, PsortbOut [File], Proteins [File], Species
SignalPApp
Annotate SignalP: Signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences
Name, Proteins
Name, Proteins [File], signalpOut [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
HifiasmApp
Assemble Hifiasm long read genome assembler
Name, Read1
Name, Reads, Draft [File]
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
DiffMethylationApp
DifferentialMethylation Finding differentially methylated regions via
Name, COV
Name, Report [Link], ResultFolder [File]
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], DupMetrics [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]
MemeApp
Motif Perform motif discovery on DNA, RNA or protein datasets
Name, PeakSequences
Name, MEME Result [File], MEME Report [Link]
MACS3App
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]
BamBoozleApp
Prep BAMboozle: Versatile removal of human sequence variation data for open data sharing ToolLink: https://github.com/sandberg-lab/dataprivacy
Name, BAM, refBuild, Species, paired
Name, Read1 [File], Species, Read Count
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]
AtacENCODEApp
QC A ATAC-seq and DNase-seq processing pipeline from ENCODE.
Name, Read1, Read2, Species
Name, Report [File], Stats [File], Html [Link]
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 DNA reads for multiple samples. In case of only one sample please use the DnaBamStatsApp instead.
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]
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]
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, PlateName
Name, Report [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]
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, Read1, Read2, Species
Name, Species, refBuild, refFeatureFile, featureLevel, transcriptTypes, SCDataOrigin, ResultDir [File], Report [Link], CountMatrix [Link], UnfilteredCountMatrix [Link], Read Count, AlignmentFile [Link]
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 [Link]
ScSeuratCombineApp
SingleCell The report of merged single cell samples/plates
Name, Species, refBuild, refFeatureFile, Static Report
Name, Species, Static Report [Link], Report [File], SeuratObject [Link]
ScSeuratCombinedLabelClusters
SingleCell The report of merged single cell samples/plates
Name, Species, Static Report, Report
Name, Species, Static Report [Link], Report [File], SeuratObject [Link]
ScSeuratCompareApp
SingleCell Empirical analysis of digital gene expression data in R
Name, Report, SeuratObject
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 [Link]
ScSeuratLabelClustersApp
SingleCell Single cell report
Name, Species, refBuild, SC Seurat
Name, Species, refBuild, refFeatureFile, Static Report [Link], SC Cluster Report [File], SC Seurat [Link]
VelocytoApp
SingleCell This wrapper runs velocyto in Single-library analysis mode.
Name, ResultDir, AlignmentFile
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], AlignmentFile [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]
VisiumQCApp
Spatial MultiSample Quality control after SpaceRanger
Name, Report, Slide
Name, Report [File], Report [Link], Species
EzPyzBin2CellApp
Spatial A Bin2Cell app for VisiumHD data
Name, BinnedOutputs2um, SourceImage, SpaceRanger
Name, Bin2Cell [File], Figures [Link], Anndata [Link], Stardist [Link]
EzPyzENACTApp
Spatial An ENACT app for VisiumHD data
Name, BinnedOutputs2um, SourceImage
Name, ENACT [File], Anndata [Link], TissUUmap [Link]
SpatialSeuratHDApp
Spatial Single cell report
Name, Species, refBuild, CountMatrix, ResultDir
Name, Species, refBuild, refFeatureFile, Static Report [Link], Report [File]
EzPyzAnndataReportApp
Spatial A Anndata report app for Spatial Trancriptomics data
Name, Anndata
Name, Report Folder [File], Report [Link]
SpaceRangerSegQCApp
Spatial This wrapper runs space ranger segmentation in Single-library analysis mode.
Name, Image
Name, ResultDir [File], Report [Link]
WordCountApp
Stats test applicaiton Supercalifragilisticexpialidocious!!
Name, Read1, Name, Read2
Name, Stats [File], Options
EzPyzExampleApp
Testing A test app for ezPyz
Name, ResultDir, IsTest
Name, Report [File], Report [Link], Species
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
Mutect2App
Variants Somatic variant calling for DNA-seq
Name, BAM, BAI, CtrlBam, refBuild
Name, VCF [File], VCFINDEX [File], Other [File], Species, refBuild
PbsvApp
Variants pbsv - PacBio structural variant (SV) calling and analysis tools
Name, BAM, BAI, refBuild
Name, refBuild, OutDir [File], OutReport [Link]
