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]
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
STARFeatureCountsApp Ultafast spliced alignment
Name, Read1, Species Name, Count [File], Stats [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]
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]
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