Modules

Category	Module	Software	Description
Preprocessing	Format::Demultiplex	cqstools fastq_demultiplex	Demultiplexing the fastq file based on barcodes
	CQS::FastqTrimmer	cqstools fastq_trimmer	Trimming 'N' from both 5' and 3' terminal of reads
	Trimmer::Cutadapt	cutadapt	Removing adapter sequences from reads
Mapping	Alignment::BWA	bwa	Bwa genome mapping algorithm
	Alignment::Bowtie1	bowtie1	Bowtie1 genome mapping algorithm
	Alignment::Bowtie2	bowtie2	Bowtie2 genome mapping algorithm
	Alignment::Tophat2	tophat2	Tophat2 RNAseq data assembler
Refinement	GATK::Refine	gatk	Realignment, base calibration and removing duplication
QC	QC::FastQC	fastqc	Quality control of fastq file
	QC::RNASeQC	RNASeQC	Quality control of bam file
Count	Count::HTSeqCount	HTSeq-count	Counting gene reads
	Count::DexseqCount	DEXSeq	Count exon reads
Summarize	CQS::CQSDatatable	cqstools data_table	Build count table from multiple counting result
Comparison	Comparison::DESeq2	DESeq2	Differential expression comparison of count data
	Cufflinks::Cufflinks	cufflinks	Transcript assembly, differential expression, and differential regulation for RNA-Seq
	Cufflinks::Cuffmerge	cuffmerge
	Cufflinks::Cuffdiff	cuffdiff
Variants	GATK::MuTect	mutect	Somatic mutation caller
	GATK::SNPIndel	gatk	SNP, indel caller
	VarScan2::Mpileup2snp	Varscan2	SNP caller
	VarScan2::Somatic	Varscan2	Somatic mutation caller
Annotation	Annotation::Annovar	annovar	Annotating SNP, indel and somatic mutation