HomerDiffPeaksApp
ATAC Finding Peaks and Differential Peaks with or without Replicates from HOMER.
Name, BAM
Name, Report [File], DiffPeak [Link]
ProkkaApp
Annotate Prokka: rapid prokaryotic genome annotation
Name, Draft
Name, ProkkaOut [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
AllPathsApp
Assemble Genome deNovo assembler based on AllPaths .
file, library_name, project_name, organism_name, type, paired, frag_size, frag_stddev, insert_size, insert_stddev, read_orientation, genomic_start, genomic_end
Name, Fasta [File], Report [File], Stats [File]
TrinityApp
Assemble RNA-seq de novo Assembly
Name, Read1, Species
Name, Fasta [File], Stats [File], Abundance Counts [File], Abundance TPM [File], Abundance TMM [File], ExN50 [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
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]
SCEdgeRApp
Differential_Expression Empirical analysis of digital gene expression data in R
Name, Species, refBuild, dummy
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]
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]
Bowtie2TranscriptomeApp
Map Aligns the reads to a transcriptome only index. The index is built from the gtf file specified. For alignments to
Name, Read1, Species
Name, trBAM [File], trBAI [File], Species, refBuild, paired, refFeatureFile, strandMode, Read Count
BowtieApp
Map Fast and memory-efficient short read aligner
Name, Read1, Species
Name, BAM [File], BAI [File], IGV [Link], Species, refBuild, paired, Read Count, IGV [File], PreprocessingLog [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]
DADA2Step1SampleApp
Metagenomics Data preprocssing with DADA2. Please make sure that the input files are from the same technology and adjust minLen and maxLen accordingly.
Name, Read1
Name, OTUsToTaxonomyFile [File], OTUsCountTable [File], RObjectPhyloseq [File], RObjectQCChimera [File]
MegahitApp
Metagenomics Denovo metagenomics assembly with Megahit.
Name, Read1
Name, contigFile [File], mappingFile [File]
MetagenomeAtlasApp
Metagenomics Data preprocssing with Metagenome Atlas. The input is short reads, requires both R1 and R2 reads and assembles genomes found in the sample.
Name, Read1, Read2
Name, Static Report [Link], Report [File]
MetaspadesApp
Metagenomics Denovo metagenomics assembly with Metaspades, gene prediction with Prodigal and annotation with InterProScan (soon also Diamond).
Name, Read1
Name, contigFile [File], prodigalPredictionFile [File], interproscanFile [File], binSummaryFile [File]
MetatranscriptomicsAnalysisApp
Metagenomics Analysis of metatranscriptomics data produced by Samsa2.
Name, annotationFileRefSeq
Name, Report [File], Static Report [Link]
MothurApp
Metagenomics Data preprocssing with Mothur. Please make sure that the input files are from the same technology and adjust minLen and maxLen accordingly.
Name, Read1
Name, OTUsToTaxonomyFile [File], OTUsCountTable [File], RObjectPhyloseq [File], RObjectQCChimera [File]
MothurStep1SampleApp
Metagenomics Data preprocssing with Mothur. Please make sure that the input files are from the same technology and adjust minLen and maxLen accordingly.
Name, Read1, Adapter1
Name, OTUsToTaxonomyFile [File], OTUsCountTable [File], RObjectPhyloseq [File], RObjectQCChimera [File]
MothurStep1SampleReportApp
Metagenomics Report of the preprocessin analysis performed with Mothur.
Name, RawDataSummary, DeduppedSummary, LenAndHomopSummary
Name, Report [File], Static Report [Link]
PhyloSeqAnalysisApp
Metagenomics 16S metagenomics visualization with Phyloseq.
Name, RObjectPhyloseq, RObjectQCChimera
Name, Static Report [Link], Report [File]
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]
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]
CisTransApp
Polyploid CisTrans detects cis- and trans-regurated genes by comparing parental diploids and polyploid expression data.
Name, Results
Name, Results [File]
FlashApp
Prep Fast Length Adjustment of SHort reads
Name, Read1, Read2
Name, Read1 [File], FlashLog [File], TrimmomaticLog [File], Species, Read Count
MergeRunDataApp
Prep Merging fastq files from two illumina runs by name
Name, Species, Read1
Name, Result [File]
TrimmomaticApp
Prep Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
Name, Read1
Name, Read1 [File], Read Count
InlineBarcodeDmxApp
Prep Simple R based app which performs demultiplexing of inline barcodes, read trimming and read filtering based on remaining read length
Name, Read1, indexFile
Name, Report [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]
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, Report [File], Html [Link], MultiQC [Link]
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]
BamPreviewApp
QC Run a mapper and compute stats on the bam files
Name, Read1, Species
Name, Report [File], Html [Link], Species, refBuild, refFeatureFile
Cov19QcApp
QC Simple quality control for Cov19 data
Name, Read1
Name, Report [File], Html [Link]
KmergenieApp
QC Kmergenie calculates kmer distribution, and it estimates the best kmer size and genome size
Name, Read1
Name, Report [Link], Results [File]
MetaQuastApp
QC MetaQUAST evaluates and compares metagenome assemblies based on alignments to close references
Name, Draft
Name, QuastReport [Link], QuastOut [File], Species
TeqcApp
QC Quality control for target capture experiments
Name, BAM, BAI, refBuild
Name, Report [File], Html [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
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]
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
BeeNetApp
SingleCell This wrapper runs BeeNet , a custom software designed to process data from paired-end Illumina® sequencing of single-cell RNA-seq libraries produced by the HIVE scRNAseq Processing Kit.
Name, Read1, Read2, Species
Name, Species, refBuild, refFeatureFile, featureLevel, transcriptTypes, ResultDir [File], CountMatrix [Link], Read Count
SingleCellCountsApp
SingleCell Maps all read files specified by the dataset file generates stats and expression counts with featureCounts
Name, ReadDataset, Species
Name, CountDataset [File], CountMatrix [File], CountFolder [File], CellCyclePhase [File], Species, refBuild, paired, refFeatureFile
SpaceRangerAggrApp
SpatialTrx 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
SpatialTrx 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 [File]
SpatialSeuratApp
SpatialTrx Single cell report
Name, Species, refBuild, CountMatrix, ResultDir
Name, Species, refBuild, refFeatureFile, Static Report [Link], Report [File]
SpatialSeuratSlidesApp
SpatialTrx Combine multiple slides from Visium/plates
Name, Species, refBuild, refFeatureFile, Static Report
Name, Species, Static Report [Link], Report [File]
SplitAndClusterApp
Special Joins the paired end files, and then splits the joined file by internal forward and reverse primers.
Name, Read1, Read2
Name, Clustered [File]
WordCountApp
Stats test applicaiton Supercalifragilisticexpialidocious!!
Name, Read1
Name, Stats [File], Options
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]
GATKv4GenerateTranscriptsFromVCFApp
Variants filtering out SNPs by the VCF coming from reference accession
Name, BAM, Filtered VCF, Species, refBuild
Name, New Genome Fasta [File], New Genome Masked Fasta [File], New Genes Annotation [File], Transcripts Fasta [File], Transcripts Masked Fasta [File], Species, refBuild, Script1 [File], Script2 [File]
ONTwfArticApp
Variants wf-artic: a Nextflow workflow for running the ARTIC SARS-CoV-2 workflow on multiplexed MinION, GridION, and PromethION runs
Name, Read1, SampleSheet
Name, ResultDir [File], Report [Link]
PCAMDSApp
Variants vcf-stats
Name, Filtered VCF, Grouping File
Name, Report [File], Static Report [Link], Interactive report [Link]
VcfStatsApp
Variants vcf-stats
Name, Filtered VCF, Dummy
Name, Report [File], Html [Link]
