SUSHI Applications

Name	Description	Required Columns	Next DataSet Columns
HomerDiffPeaksApp	Finding Peaks and Differential Peaks with or without Replicates from HOMER.	Name, BAM	Name, Report [File], DiffPeak [Link]
AtacENCODEApp	A ATAC-seq and DNase-seq processing pipeline from ENCODE.	Name, Read1, Read2, Species	Name, Report [File], Stats [File], Html [Link]
ProkkaApp	Prokka: rapid prokaryotic genome annotation	Name, Draft	Name, ProkkaOut [File], Species
ProdigalApp	Prodigal: rapid prokaryotic genome annotation	Name, Draft	Name, Out [File], Proteins [File], Species
PsortbApp	Psortb: subcellular protein localization prediction tool for Bacteria and Archea	Name, Proteins	Name, PsortbOut [File], Species
AllPathsApp	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]
CanuApp	Canu long read genome assembler	Name, Read1	Name, Reads, Draft [File], CanuOut [File]
SpadesApp	SPAdes genome assembler	Name, Read1	Name, Draft [File], SpadesOut [File], SpadesLog [File], PreprocessingLog [File], Species, Read Count
TrinityApp	RNA-seq de novo Assembly	Name, Read1, Species	Name, Fasta [File], Stats [File], Abundance Counts [File], Abundance TPM [File], Abundance TMM [File], ExN50 [File]
UnicyclerApp	Unicycler microbial genome assembler	Name, Read1	Name, Draft [File], Graph [File], Log [File], Species, Read Count
ExceRptApp	Annotation and Profiling of smallRNA-seq with exceRpt's pipeline	Name, Read1, Adapter1, Species	Name, excerpt [File], Species, refBuild
FeatureCountsApp	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	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 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	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	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	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	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	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	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]
Bowtie2TranscriptomeApp	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	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]
STARApp	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]
Pbmm2App	A minimap2 frontend for PacBio native data formats	Name, Read1	Name, BAM [File], BAI [File], IGV [Link], refBuild, IGV [File], Pbmm2Log [File]
DADA2Step1SampleApp	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]
KrakenApp	Kraken taxonomic sequence classification system	Name, Read1	Name, KronaReport [Link], KrakenOut [File], KrakenReport [File], KronaOutDir [File], KronaOut [File]
MegahitApp	Denovo metagenomics assembly with Megahit.	Name, Read1	Name, contigFile [File], mappingFile [File]
MetaspadesApp	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	Analysis of metatranscriptomics data produced by Samsa2.	Name, annotationFileRefSeq	Name, Report [File], Static Report [Link]
MothurApp	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	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	Report of the preprocessin analysis performed with Mothur.	Name, RawDataSummary, DeduppedSummary, LenAndHomopSummary	Name, Report [File], Static Report [Link]
PhyloSeqAnalysisApp	16S metagenomics visualization with Phyloseq.	Name, RObjectPhyloseq, RObjectQCChimera	Name, Static Report [Link], Report [File]
VirDetectApp	Virome analysis for the diagnostic use in veterinary virology	Name, Read1, Species	Name, Species, virBuild, hostBuild, paired, Read Count, OutDir [File], OutReport [Link]
MetagenomeAtlasApp	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]
QIIME2App	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]
PostSamsa2AnalysisApp	Step_6 of Samsa2, data analysis and report.	Name, annotationORGFileRefSeq, annotationFUNCFileRefSeq	Name, Report [File], Static Report [Link]
Samsa2App	Metatranscriptomics pipeline with Samsa2.	Name, Read1	Name, annotationFileRefSeq [File], annotationORGFileRefSeq [File], annotationFUNCFileRefSeq [File]
CountSpacerApp	QC Tool for sgRNA libraries.	Name, Read1	Name, Report [File], Html [Link], Count [File], Species, Read Count
MageckCountApp		Name, Read1	Name, Count [File], Log [File], Read Count, libName, Species
NestLinkApp	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	Perform motif discovery on DNA, RNA or protein datasets	Name, PeakSequences	Name, MEME Result [File], MEME Report [Link]
MACS2App	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]
CisTransApp	CisTrans detects cis- and trans-regurated genes by comparing parental diploids and polyploid expression data.	Name, Results	Name, Results [File]
ConvERDSApp	This converts the result DataSet of EAGLERCApp to an input DataSet of DNAHaplotypeCallerGVCFApp.	Name, Species, dummy	Name, BAM, refBuild, Species, Dummy [File]
EAGLERCApp	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	Merging two DataSets	Name, BAM, refBuild, Species	Name, BAM1, BAM2, refBuild1, refBuild2, Species, dummy [File]
FlashApp	Fast Length Adjustment of SHort reads	Name, Read1, Read2	Name, Read1 [File], FlashLog [File], TrimmomaticLog [File], Species, Read Count
InlineBarcodeDmxApp	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]
MergeRunDataApp	Merging fastq files from two illumina runs by name	Name, Species, Read1	Name, Result [File]
TrimmomaticApp	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
EnaApp	Download public data from ENA	Name, projectID	Name, projectID, ENA Result [File]
BamPreviewApp	Run a mapper and compute stats on the bam files	Name, Read1, Species	Name, Report [File], Html [Link], Species, refBuild, refFeatureFile
CountQCApp	Quality control after counting reads	Name, Count, Species, refBuild, featureLevel, refFeatureFile	Name, Species, refBuild, Static Report [Link], Live Report [Link], Report [File]
Cov19QcApp	Simple quality control for Cov19 data	Name, Read1	Name, Report [File], Html [Link]
DnaBamStatsApp	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	Quality control after the alignment of RNAseq reads	Name, BAM, BAI, refBuild, Species	Name, Report [File], Html [Link], Species, refBuild, refFeatureFile
ExceRptReportApp	QC report of exceRpt outputs.	Name, excerpt, Species, refBuild	Name, Species, refBuild, Static Report [Link], Report [File]
FastqScreen10xApp	Screen files for contaminations or ribosomal RNA content	Name, RawDataDir, Read Count	Name, Report [File], Html [Link]
FastqScreenApp	Screen files for contaminations or ribosomal RNA content	Name, Read1, Read Count	Name, Report [File], Html [Link]
Fastqc10xApp	A quality control tool for NGS reads	Name, RawDataDir, Read Count	Name, Report [File], Html [Link], MultiQC [Link]
FastqcApp	A quality control tool for NGS reads	Name, Read1	Name, Report [File], Html [Link], MultiQC [Link]
KmergenieApp	Kmergenie calculates kmer distribution, and it estimates the best kmer size and genome size	Name, Read1	Name, Report [Link], Results [File]
MageckTestApp	Run test module in the tool Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK)	Name, Count	Name, Report [File], Report [Link]
QuastApp	QUAST (Quality Assessment Tool for Genome Assemblies)	Name, Draft	Name, QuastReport [Link], QuastOut [File], Species
RnaBamStatsApp	Quality control after the alignment of RNAseq reads	Name, BAM, BAI, refBuild, Species	Name, Report [File], Html [Link], Species, refBuild, refFeatureFile
TeqcApp	Quality control for target capture experiments	Name, BAM, BAI, refBuild	Name, Report [File], Html [Link]
NanoPlotApp	NanoPlot: Plotting tool for long read sequencing data and alignments	Name, Read1	Name, NanoPlot Result [File], Report [Link]
CrisprScreenQCApp	Screens of CRISPR samples for contaminations	Name, Read1	Name, Report [File], Html [Link]
RnaBiasApp		Name, Read1, Species	Name, Report [File], Report [Link]
PreqcApp	Preqc - Illumina read pre-assembly quality control and data exploration module within sga	Name, Read1, Read2	Name, PreqcReport [Link], PreqcReport [File], PreqcOut [File]
BuscoApp	BUSCO: from QC to gene prediction and phylogenomics	Name, Draft	Name, BuscoPlot [Link], BuscoOut [File], Species
GceApp	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]
MetaQuastApp	MetaQUAST evaluates and compares metagenome assemblies based on alignments to close references	Name, Draft	Name, QuastReport [Link], QuastOut [File], Species
ExploreMageckCountsApp	Quality control after counting sgRNAs with Mageck	Name, Count, Species	Name, Species, libName, Static Report [Link], Live Report [Link], Report [File]
CellRangerAggrApp	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	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
MergeSCDataSetsApp	Merging more than two DataSets generaged from same library for CellRangerApp	Name, Species, RawDataDir	Name, Species
SCFeatBarcodingApp	Single cell report	Name, Species, refBuild, CountMatrix, ResultDir	Name, Species, refBuild, refFeatureFile, Static Report [Link], Report [File]
ScSeuratApp	Single cell report	Name, Species, refBuild, CountMatrix, ResultDir, Condition	Name, Species, refBuild, refFeatureFile, Static Report [Link], SC Cluster Report [File], SC Seurat
SCTrajectoryInferenceApp	Trajectory inference analysis for single cell data	Name, Static Report	Name, Report [File], Static Report [Link]
STARsoloApp	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]
SingleCellCountsApp	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
ScSeuratCombineApp	The report of merged single cell samples/plates	Name, Species, refBuild, refFeatureFile, Static Report	Name, Species, Static Report [Link], Report [File]
VelocytoApp	This wrapper runs velocyto in Single-library analysis mode.	Name, ResultDir	Name, LOOM [File], Species, refBuild, refFeatureFile, featureLevel, Read Count
ScSeuratCompareApp	Empirical analysis of digital gene expression data in R	Name, Report	Name, Static Report [Link], Report [File]
ONTwfScApp	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]
CellRangerMultiApp	This wrapper runs cellranger multi in Single-library analysis mode.	Name, RawDataDir, Species	Name, Species, refBuild, refFeatureFile, featureLevel, transcriptTypes, SCDataOrigin, ResultDir [File], Read Count
BDRhapsodySAApp	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
BeeNetApp	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
ScSeuratFilterClustersApp	Single cell report	Name, Species, refBuild, SC Seurat	Name, Species, refBuild, refFeatureFile, Static Report [Link], SC Cluster Report [File], SC Seurat
ScSeuratLabelClustersApp	Single cell report	Name, Species, refBuild, SC Seurat	Name, Species, refBuild, refFeatureFile, Static Report [Link], SC Cluster Report [File], SC Seurat
ScSeuratCombinedLabelClusters	The report of merged single cell samples/plates	Name, Species, Static Report, Report	Name, Species, Static Report [Link], Report [File]
SpaceRangerApp	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	Single cell report	Name, Species, refBuild, CountMatrix, ResultDir	Name, Species, refBuild, refFeatureFile, Static Report [Link], Report [File]
SpatialSeuratSlidesApp	Combine multiple slides from Visium/plates	Name, Species, refBuild, refFeatureFile, Static Report	Name, Species, Static Report [Link], Report [File]
SpaceRangerAggrApp	This wrapper runs spaceranger aggr in multi-library analysis mode.	Name, CountMatrix	Name, Species, refBuild, refFeatureFile, featureLevel, transcriptTypes, ResultDir [File], Report [Link], CountMatrix [Link]
SplitAndClusterApp	Joins the paired end files, and then splits the joined file by internal forward and reverse primers.	Name, Read1, Read2	Name, Clustered [File]
WordCountApp	test applicaiton Supercalifragilisticexpialidocious!!	Name, Read1	Name, Stats [File], Options
GATKv4DNAHaplotypeCallerGVCFApp	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	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	genotype,merge and annotate gvcf-Files	Name, GVCF, GVCFINDEX, Species, refBuild, Dummy	Name, Raw VCF [File], Filtered VCF [File], Species, refBuild
GATKv4GenerateTranscriptsFromVCFApp	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]
GATKv4JointGenoTypesApp	genotype,merge and annotate gvcf-Files	Name, GVCF, GVCFINDEX, Species, refBuild, Dummy	Name, Raw VCF [File], Filtered VCF [File], Species, refBuild
GatkDnaHaplotyperApp	Haplotype calling for DNA-seq	Name, BAM, BAI, refBuild	Name, GVCF [File], GVCFINDEX [File], Species, targetFile, refBuild
GatkJoinGenoTypesApp	genotype,merge and annotate gvcf-Files	Name, GVCF, GVCFINDEX, Species, refBuild	Name, Report [File], Species, refBuild
GatkRnaHaplotyperApp	Haplotype calling for RNA-seq	Name, BAM, BAI, refBuild	Name, GVCF [File], GVCFINDEX [File], Species, refBuild
MpileupApp	Variant analysis with samtools/bcftools.	Name, BAM, BAI, refBuild, Species	Name, VCF [File], TBI [File], Report [File], Html [Link], Species, refBuild
VcfStatsApp	vcf-stats	Name, Filtered VCF, Dummy	Name, Report [File], Html [Link]
PbsvApp	pbsv - PacBio structural variant (SV) calling and analysis tools	Name, BAM, BAI, refBuild	Name, refBuild, OutDir [File], OutReport [Link]
PCAMDSApp	vcf-stats	Name, Filtered VCF, Grouping File	Name, Report [File], Static Report [Link], Interactive report [Link]
ONTwfArticApp	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]