. 2014 May 8;42(Web Server issue):W494–W500. doi: 10.1093/nar/gku370

Table 3.

Running time (in min) for reporting n mapping locations per read

Software	n = 100	n = 1000	n = ∞
mrsFAST-Ultra	58	62	71
BWA	69	69	80
Bowtie2^a	35	420	NA
GEM^b	14	15	16
RazerS3	382	420	528
GSNAP	183	184	184
SRmapper	166	166	166

^aBowtie2 cannot complete the task in 12 h with the -a option.

^bNote that although GEM provides the best speed, it has lower sensitivity and has a higher memory requirement in comparison to mrsFAST-Ultra (4.1GB versus 2.5GB).