SUSHI Applications


NameAnalysis CategoryDescriptionRequired ColumnsNext DataSet Columns
DEXSeqApp Inference of differential exon usage in RNA-Seq
Name, BAM, BAI, Species, refBuild, refFeatureFile Name, Species, refBuild, Report [File], Html [Link]
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]
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]
SpadesApp SPAdes genome assembler Name, Read1 Name, Draft [File], SpadesOut [File], SpadesLog [File], TrimmomaticLog [File], Species, Read Count
CanuApp Canu long read genome assembler Name, Reads Name, Reads, Draft [File], CanuOut [File]
HGAPApp The Hierarchical Genome Assembly Process (HGAP) from SMRT Analysis Name, Reads Name, Reads, Static Report [Link], Draft [File], HGAPOut [File]
DiscovarDenovoApp DISCOVAR de novo is a large (and small) de novo genome assembler. It quickly generates highly accurate and complete assemblies using the same single library data as used by DISCOVAR. It currently doesn’t support variant calling – for that, please use DISCOVAR instead. Name, Read1 Name, Results [File]
NcPROApp Annotation and Profiling of ncRNAs in smallRNA-seq
Name, Read1, Adapter1, Species Name, Species, refBuild, Report [File], Html [Link], TrimCounts [Link]
RSEMApp Use bowtie alignments to transcript database and a posterior model to estimate isoform/gene abundances
Name, Read1, Species Name, Count [File], Species, refBuild, featureLevel, refFeatureFile, strandMode, paired, Read Count, transcriptTypes, PreprocessingLog [File]
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
SalmonApp Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Name, Read1, Species Name, Count [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], Species, refBuild, featureLevel, refFeatureFile, strandMode, paired, Read Count, transcriptTypes
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]
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]
BWAApp Burrows-Wheeler Aligner
Name, Read1, Species Name, BAM [File], BAI [File], IGV Starter [Link], Species, refBuild, paired, refFeatureFile, strandMode, Read Count, IGV Starter [File], IGV Session [File], PreprocessingLog [File]
Bowtie2App Fast and sensitive read alignment. Supports local and end-to-end mode
Name, Read1, Species Name, BAM [File], BAI [File], IGV Starter [Link], Species, refBuild, paired, Read Count, IGV Starter [File], IGV Session [File], PreprocessingLog [File], Bowtie2Log [File]
BowtieApp Fast and memory-efficient short read aligner
Name, Read1, Species Name, BAM [File], BAI [File], IGV Starter [Link], Species, refBuild, paired, Read Count, IGV Starter [File], IGV Session [File], PreprocessingLog [File]
STARApp Ultafast spliced alignment
Name, Read1, Species Name, BAM [File], BAI [File], IGV Starter [Link], Species, refBuild, paired, refFeatureFile, strandMode, Read Count, IGV Starter [File], IGV Session [File], PreprocessingLog [File], STARLog [File]
TophatApp A spliced read mapper for RNA-Seq
Name, Read1, Species Name, BAM [File], BAI [File], IGV Starter [Link], Species, refBuild, paired, refFeatureFile, strandMode, Read Count, IGV Starter [File], IGV Session [File], PreprocessingLog [File]
BismarkApp A tool to map bisulfite converted sequence reads and determine cytosine methylation states
Name, Read1, Adapter1, 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]
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
ReseqApp Resequencing pipeline (read alignment, variant calling, consensus polishing) from SMRT Analysis Name, Reads Name, BAM [File], BAI [File], VCF [File], Static Report [Link], VCFINDEX [File], Consensus [File], ResequencingOut [File]
VirDetectApp Virome analysis for the diagnostic use in veterinary virology
Name, Read1, Read2, Species Name, Species, virBuild, hostBuild, paired, Read Count, OutDir [File], OutReport [Link]
MothurDataCleanApp OTU-based metagenomics analysis with Mothur. Name, Read1, Read2 Name, Static Report [Link], SubreadsOut [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, Control Name, Species, refBuild, refFeatureFile, paired, CalledPeaks [File], BED [File], PeakSequences [File], BigWigFile [File]
ReadClassifyApp ReadClassifyApp does the mapped read classification depending on the number of mismatch. ReadClassifyApp calls 'read_clasify.py' script. Name, BAM1, BAM2, refBuild1, refBuild2, Species Name, Parent1OrigBAM [File], Parent1OrigBAI [File], Parent1OtherBAM [File], Parent1OtherBAI [File], Parent1CommonBAM [File], Parent1CommonBAI [File], refBuild1, Parent2OrigBAM [File], Parent2OrigBAI [File], Parent2OtherBAM [File], Parent2OtherBAI [File], Parent2CommonBAM [File], Parent2CommonBAI [File], refBuild2, Species, dummy [File]
MergeDataSetApp Merging two DataSets

Name, BAM, refBuild, Species Name, BAM1, BAM2, refBuild1, refBuild2, Species, dummy [File]
ConvRCDSApp This converts the result DataSet of ReadClassifyApp to an input DataSet of CountQCApp. Name, Species, dummy, Condition Name, BAM, BAI, refBuild, Species, dummy [File], Condition [Factor]
HomeoRoqApp HomeoRoq detects the significant genes that homeolog ratio changes in a target condition.
Name, Report, Dummy Name, Results [File]
CisTransApp CisTrans detects cis- and trans-regurated genes by comparing parental diploids and polyploid expression data.
Name, Results Name, Results [File]
FlashApp Fast Length Adjustment of SHort reads Name, Read1, Read2 Name, Read1 [File], FlashLog [File], TrimmomaticLog [File], Species, Read Count
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], Adapters [File]
TranscriptCoverageApp Compute the base-by-base coverage from transript alignment files. Name, trBAM, trBAI, refBuild Name, Count [File], Profiles [File], Species, refBuild, refFeatureFile, featureLevel, strandMode, paired, Read Count, coverageType
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]
TeqcApp Quality control for target capture experiments
Name, BAM, BAI, refBuild Name, Report [File], Html [Link]
FastqcApp A quality control tool for NGS reads
Name, Read1 Name, Report [File], Html [Link]
CountQCApp Quality control after counting reads
Name, Count, Species, refBuild, featureLevel, refFeatureFile Name, Species, refBuild, Static Report [Link], Live Report [Link], Report [File]
FastqScreenApp Screen files for contaminations or ribosomal RNA content
Name, Read1, Read Count Name, Report [File], Html [Link]
RnaBamStatsApp Quality control after the alignment of RNAseq reads
Name, BAM, BAI, refBuild Name, Report [File], Html [Link], Species, refBuild, refFeatureFile
BamPreviewApp Run a mapper and compute stats on the bam files
Name, Read1 Name, Report [File], Html [Link], Species, refBuild, refFeatureFile
KmergenieApp Kmergenie calculates kmer distribution, and it estimates the best kmer size and genome size
Name, Read1 Name, Report [Link], Results [File]
SubreadsApp Subreads from SMRT Analysis Name, Reads Name, Read1 [File], Static Report [Link], SubreadsOut [File]
QuastApp QUAST (Quality Assessment Tool for Genome Assemblies) Name, Draft Name, QuastReport [Link], QuastOut [File], Species
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
ScaterApp Maps all read files specified by the dataset file generates stats and expression counts with featureCounts Name, CountDataset, CountMatrix, Species Name, Species, refBuild, Static Report [Link], Live Report [Link], Report [File]
SCCountsApp Maps unmapped bam file with STAR and generates stats and expression counts with featureCounts Name, Read1, Species, CellDataset Name, Species, refBuild, paired, refFeatureFile, transcriptTypes, CellDataset [File], CountMatrix [File], Stats [File], CellCyclePhase [File], BAM [File], BAI [File], PreprocessingLog [File], STARLog [File]
SplitAndClusterApp Joins the paired end files, and then splits the joined file by internal forward and reverse primers. Name, Read1, Read2 Name, Clustered [File]
MpileupApp Variant analysis with samtools/bcftools.
Name, BAM, BAI, refBuild Name, VCF [File], TBI [File], IGV Starter [Link], Report [File], Html [Link], Species, refBuild, IGV Starter [File], IGV Session [File]
VariantCallerApp Variant caller and variant annotator starting from a bam file. Name, BAM, BAI, refBuild Name, VCF [File], BAM [File], BAI [File], Gene_summary [File], Html [Link,File], refBuild
GatkRnaHaplotyperApp Haplotype calling for RNA-seq
Name, BAM, BAI, build Name, VCF [File], TBI [File], Report [File], Html [Link], Species, build
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
GatkRnaApp Variant calling for RNA-seq using GATK Queue and recommended filtering. Name, BAM, BAI, refBuild Name, VCF [File], VCF_index [File], Species, refBuild