Table 2.

RNAseq preprocessing and analysis tools currently in common use.

Tool type	Tool name	Reference
Quality Control	FastQC	Andrews, 2010
	RNA-SeQC	DeLuca et al., 2012
	RSeQC	Wang et al., 2012
	ShortRead	Morgan et al., 2009
Trimming, Demultiplexing	FASTX-Toolkit	http://hannonlab.cshl.edu/fastx_toolkit
	Stacks	Catchen et al., 2011
	Trimmomatic	Bolger et al., 2014
	TrimGalore	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
General aligners, Psuedoaligners, De novo Annotators	Bowtie2	Langmead and Salzberg, 2012
	Kallisto	Bray et al., 2016
	Novalign	http://www.novocraft.com
	SOAP2	Li R. et al., 2009
	STAR	Dobin et al., 2013
	Tophat2	Kim D. et al., 2013
Post-Alignment Processing, QC, Counting, and Visualization	htseq-count	Anders et al., 2013
	IGV	Thorvaldsdottir et al., 2013
	RNA-SeQC	DeLuca et al., 2012
	RSeQC	Wang et al., 2012
	Rsubread	Liao et al., 2013
	SAMtools	Li H. et al., 2009
Differential Expression Analysis	edgeR	Robinson et al., 2010
	DESeq2	Anders et al., 2013
	baySeq	Hardcastle and Kelly, 2010
	Cuffdiff2	Trapnell et al., 2013
	DEGseq	Wang et al., 2010
	EBSeq	Leng et al., 2013, 2015
	voom	Law et al., 2014