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Table 1 Parameters used in the two experiments for each of the aligners tested

From: Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data

Mapper Parameters
GNUMAP-bs -m 17 -s 1 -T 20 -a 0.90 (-a 0.92) -b
Novoalign -k 17 -s 2 -r -A 20 -t 75 (-t 90) -b2
BSMAP -n 0 -w 100 -v 3
Bismark -n 2 -l 50
Bismark-bt2 -N 1 -L 20 -bowtie2 -min-score L,0,-0.6
LAST -Q1 -j1 -d120 -n20 -f1 | -s150 -m0.95
BRAT-BW default settings for single-end reads
  1. Parameters in parentheses were used for the human BSR dataset. Up to 3 to 4 sequencing errors or mutations were allowed in a 100-bp long BSR. Because the human genome contains many repeated genomic regions, 20 valid mapping locations were allowed for a given read when the alignment method supported this feature.