Table 1

Chromosome 1 Bis-SNP detection

Sample

Aligner

reference

cvg

Het SNPs

Hom SNPs

Callable bases

runtime

OTB

MAQ

hg18

32×

119,103

67,725

211,042,010

2.8 h

TCGA-lung-normal

BSMAP

hg19

19×

118,412

58,309

222,763,786

3.1 h

TCGA-breast-normal

BSMAP

hg19

19×

113,009

57,281

221,014,965

2.7 h

Mouse-F1i

Novoalign

mm9

50×

663,528

65,364

178,718,615

3.1 h

Mouse-F1r

Novoalign

mm9

41×

682,979

67,068

178,847,508

3.1 h

Notes: All benchmarking performed using a single Intel(R) Xeon (X5650,2.67 GHz) server with 12 CPU cores and 10 GB memory. SE refers to single-end sequencing and PE to paired-end.

Liu et al. Genome Biology 2012 13:R61   doi:10.1186/gb-2012-13-7-r61