Figure 2

Benchmarking of programs on various simulated and real data sets. (a) Benchmark results of BatMeth and other methods on the simulated reads: A, BatMeth; B, BSMAP; C, BS-Seeker; D, Bismark. The timings do not include index/table building time for BatMeth, BS-Seeker, and Bismark. These three programs only involve a one-time index-building procedure but BSMAP rebuilds its seed-table upon every start of a mapping procedure. (b) Insert lengths of uniquely mapped paired reads and the running times for the compared programs. (c) Benchmark results on simulated SOLiD reads. Values above the bars are the percentage of false positives in the result sets. The numbers inside the bars are the number of hits returned by the respective mappers. The graph on the right shows the running time. SOCS-B took approximately 16,500 seconds and is not included in this figure. (d) bisulfite and non-bisulfite induced (SNP) adjacent color mismatches.