Name	Analysis Category	Description	Required Columns	Next DataSet Columns
TrinityApp	Assemble	RNA-seq de novo assembly	"Name, Read1, Species"	"Name, Fasta [File]"
AllPathsApp	Assemble	Genome de novo assembler	"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]"
RSEMApp	Count	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"
NcPROApp	Count	Annotation and Profiling of ncRNAs in smallRNA-seq	"Name, Read1, Adapter1, Species"	"Name, Species, refBuild, Report [File], Html [Link], TrimCounts [Link]"
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"
STARFeatureCountsApp	Demo	Ultafast spliced alignment	"Name, Read1, Species"	"Name, Count [File], Stats [File], Species, refBuild, featureLevel, refFeatureFile, strandMode, paired, Read Count"
DESeq2App	Differential_Expression	Differential gene expression analysis based on the negative binomial distribution	"Name, Count, Species, refBuild, featureLevel, refFeatureFile"	"Name, Species, refBuild, Report [File], Html [Link]"
EdgeRApp	Differential_Expression	Empirical analysis of digital gene expression data in R	"Name, Count, Species, refBuild, featureLevel, refFeatureFile"	"Name, Species, refBuild, Report [File], Html [Link]"
BWAApp	Map	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]"
BowtieApp	Map	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]"
Bowtie2App	Map	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]"
STARApp	Map	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]"
BismarkApp	Map	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"
TophatApp	Map	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]"
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, Control"	"Name, Species, refBuild, refFeatureFile, paired, CalledPeaks [File], BED [File], PeakSequences [File], BigWigFile [File]"
HomeoRoqApp	Polyploid	HomeoRoq detects the significant genes that homeolog ratio changes in a target condition.	"Name, Report"	"Name, Results [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, Reads [File], FlashLog [File], TrimmomaticLog [File], Species, Read Count"
CountQCApp	QC	Quality control after counting reads	"Name, Count, Species, refBuild, featureLevel, refFeatureFile"	"Name, Species, refBuild, Report [File], Html [Link]"
RnaBamStatsApp	QC	Quality control after the alignment of RNAseq reads	"Name, BAM, BAI, refBuild"	"Name, Report [File], Html [Link], Species, refBuild, refFeatureFile"
FastqScreenApp	QC	Screen files for contaminations or ribosomal RNA content	"Name, Read1"	"Name, Report [File], Html [Link]"
BamPreviewApp	QC	Run a mapper and compute stats on the bam files	"Name, Read1"	"Name, Report [File], Html [Link], Species, refBuild, refFeatureFile"
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]"
TeqcApp	QC	Quality control for target capture experiments	"Name, BAM, BAI, refBuild"	"Name, Report [File], Html [Link]"
FastqcApp	QC	A quality control tool for NGS reads	"Name, Read1"	"Name, Report [File], Html [Link]"
VariantCallerApp	Variants	Variant caller and variant annotator starting from a bam file.	"Name, BAM, BAI, refBuild"	"Name, VCF [File], Gene_summary [File], Html [Link,File], refBuild"
MpileupApp	Variants	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]"
GatkRnaSeqHaplotyperApp	Variants	Haplotype calling for RNA-seq	"Name, BAM, BAI, build"	"Name, VCF [File], TBI [File], Report [File], Html [Link], Species, build"