Designing Efficient Spaced Seeds for SOLiD Read Mapping

Table 2

Comparison of 6 read-mapping tools on S. cerevisiae 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	553,140 (43.20%)	512,086 (39.99%)	0m50s
BWA	422,550 (33.00%)	395,342 (30.87%)	0m38s
MAQ	616,497 (48.14%)	567,549 (44.32%)	1m20s
PerM	418,524 (32.68%)	347,668 (27.15%)	0m31s
SHRiMP 1.3.2	663,923 (51.85%)	—	7m56s
SHRiMP 2.0	709,146 (55.38%)	—	1m22s
STORM	839,633 (65.57%)	754,402 (58.91%)	2m10s