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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.