SUSHI Applications


NameAnalysis CategoryDescriptionRequired ColumnsNext DataSet Columns
HomerDiffPeaksApp Finding Peaks and Differential Peaks with or without Replicates from HOMER.
Name, BAM Name, Report [File], DiffPeak [Link]
ProkkaApp Prokka: rapid prokaryotic genome annotation Name, Draft Name, ProkkaOut [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]
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
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
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
SpaceRangerApp This wrapper runs space ranger count in Single-library analysis mode. Name, RawDataDir, Species, Image, Slide, Area Name, Species, refBuild, refFeatureFile, featureLevel, transcriptTypes, ResultDir [File], Report [Link], CountMatrix [Link]
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]