8,755,069 RNA-seq profiling Solexa reads were mapped to mouse whole genome with different programs. In this comparison, the maximum mismatch number threshold was set to 3 (including substitutions and indels). The comparison was run on a local Linux box with two Intel quad-core (E7310 @ 1.6 G Hz) CPUs and 64 G RAM (detailed running parameters for each tool were shown in Supplementary Table S1 of Additional File 2). To handle the physical memory limitation of some of the programs BOAT is compared to, reads were mapped against individual chromosomes sequentially. "Time" shows the sum of the execution times, and "Memory" shows the maximal memory usage among those runs.