Designing Efficient Spaced Seeds for SOLiD Read Mapping

Table 3

Comparison of 6 read-mapping tools on the E. coli dataset. The execution time refers to all steps, including index construction for the tools that can reuse the result of this step (Bowtie, BWA, MAQ).

Program	Mapped reads	Unique mapping positions	Execution time
Bowtie	456,416 (45.64%)	423,541 (42.35%)	0m18s
BWA	456,928 (45.69%)	424,239 (42.42%)	0m21s
MAQ	646,523 (64.65%)	588,362 (58.84%)	1m08s
PerM	413,102 (41.31%)	384,050 (38.40%)	0m23s
SHRiMP 1.3.2	687,855 (68.79%)	—	3m33s
SHRiMP 2.0	714,662 (71.47%)	—	0m41s
STORM	773,155 (77.32%)	697,164 (69.72%)	0m57s