Table 3.

Comparison of selected key features of the used mappers. Features indicated by X are included in the specified mapper.

	Bwa	CLC	HISAT2	Kallisto	RSEM	Salmon	STAR
Reference
Genome		X	X				X
Transcriptome	X	X	X	X	X	X	X
Needs annotation	X	X		X	X	X
Specifications
Alignment-based	X	X	X		X		X
Pseudo-alignment				X		X
Expression values		X		X	X	X	X
Splice aware		X	X				X
Commercial software		X