TABLE 4.

Widely used tools for read alignment and expression quantification.

Tool	Function	Feature	URL	References
Salmon	Expression quantification	k-mer-based read quantification	https://combine-lab.github.io/salmon/	Patro et al., 2017
Kallisto	Expression quantification	Pseudoalignment-based rapid read determination	https://pachterlab.github.io/kallisto/	Bray et al., 2016
StringTIe	Expression quantification	Alignment based, splice aware	https://ccb.jhu.edu/software/stringtie/	Pertea et al., 2015
HISAT2	Read alignment	Alignment based, splice aware	https://daehwankimlab.github.io/hisat2/	Sirén et al., 2014
Sailfish	Expression quantification	k-mer-based read quantification	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Patro et al., 2014
RNA-Skim	Expression quantification	Sig-mer (a type of k-mer)-based read quantification of transcripts	http://www.csbio.unc.edu/rs/	Zhang and Wang, 2014
TopHat2	Read alignment	Alignment based, splice aware	https://ccb.jhu.edu/software/tophat/index.shtml	Kim et al., 2013
STAR	Read alignment	Alignment based, splice aware	https://github.com/alexdobin/STAR	Dobin et al., 2013
Bowtie	Read alignment	Maintains quality threshold, hence less no. of mismatches	http://bowtie-bio.sourceforge.net/index.shtml	Langmead et al., 2009
Cufflinks	Expression quantification	Alignment based, splice aware	https://github.com/cole-trapnell-lab/cufflinks	Trapnell et al., 2010