Table 2.

A selection of short reads alignment tools. The platform compatibility depends on the maximum read length supported by the program.

Program	Author(s)	Website	Platform	Aligned Gbp per CPU day
Maq [24]	Li H	http://maq.sourceforge.net/	Illumina, SOLiD (partial)	~ 0.2
Bowtie [25]	Langmead B Et, al.	http://bowtie-bio.sourceforge.net/index.shtml	Illumina	~ 7
SSAHA2 [26]	Ning Z Et, al.	http://www.sanger.ac.uk/resources/software/ssaha2/	Illumina, SOLiD, 454	~ 0.5
BWA [27]	Li H and Durbin R	http://bio-bwa.sourceforge.net/bwa.shtml	Illumina, SOLiD, 454	~ 7
SOAP2 [28]	Li R Et, al.	http://www.sanger.ac.uk/resources/software/ssaha2/	Illumina	~ 7