Table 1.

Benchmark results of SeqMap, ELAND, SOAP and RMAP

Software	Running time	Memory used	Mapped reads
SeqMap	2213 s	3.0 GB	455 384
ELAND	345 s	721 MB	455 384
SOAP	5464 s	979 MB	452 005
RMAP	14 h	3.1 GB	321 651

11 530 816 Solexa reads (25 nt) are mapped to mouse chrX (166 650 296 bp) using SeqMap, ELAND, SOAP and RMAP, respectively. The running time, memory usage, and number of mapped reads for each program are reported. For each program, up to two substitutions are allowed and no gap is allowed. The experiments are done on a machine with 3 GHz Intel Xeon CPU and 32 GB memory, running 64-bit Linux.