Table 2. Times (in seconds) for mapping 100,000 reads of 100 bp vs genome with different programs in the four organisms analyzed.

Program	Yeast	Drosophila	Arabidopsis
BLAT	287	2868	1721
SSAHA2	29	107	76
Bowtie	50	6	8
SeqMap	16	1260	958
MAQ	50	470	376
CLC NGS Cell *	376	1232	856

^*typically the speed is improved by the parallel use of all processors of the computer.