Skip to main content

Table 2 Performance comparison of BS aligners on WGBS data

From: BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data

 

BS-Seeker2

Bismark

BSMAP

WGBS

Bowtie2

Bowtie

Bowtie2

Bowtie

 

local

e2e

(e2e)

Simulation: error-free

map

91.65%

91.50%

91.65%

87.78%

91.65%

91.81%

acc

100.00%

100.00%

100.00%

100.00%

100.00%

100.00%

Simulation: error-containing

map

91.62%

90.51%

91.69%

86.90%

91.64%

91.90%

acc

99.22%

99.73%

99.82%

99.86%

99.80%

99.82%

Real data

map

83.80%

72.94%

71.89%

70.31%

73.15%

72.84%

  1. In this table, BS-Seeker2 maps the reads to whole genome. map = mappability, acc = accuracy, local = local alignment model of Bowtie2, e2e = end-to-end alignment model of Bowtie2.