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Table 3 Performance comparison of BS aligners on RRBS data

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

  BS-Seeker2 Bismark BSMAP
RRBS Bowtie2 Bowtie Bowtie2 Bowtie (RRBSMAP)
  local e2e (e2e)
Simulation: error-free
map 78.29% 78.02% 78.29% 72.51% 78.08% 78.63%
acc 100.00% 100.00% 100.00% 100.00% 100.00% 99.82%
Simulation: error-containing
map 79.18% 78.42% 78.72% 71.36% 78.17% 79.10%
acc 98.11% 98.59% 99.02% 99.61% 98.82% 98.81%
Real data
map 64.45% 48.78% 47.29% 44.24% 46.89% 45.64%
  1. map = mappability, acc = accuracy, local = local alignment mode, e2e = end-to-end alignment mode. In this table, BS-Seeker2 maps the reads to RR genome (fragment lengths ranging 20 bp ~ 400 bp).