Default options effect using wgsim. Mapping 1 million reads of length 125 extracted from the Human genome using wgsim. Each tool was allowed to use its own default options. BWA-ND refers to BWA’s results while using Bowtie’s default options which are 2 mismatches in the seed, 3 mismatches in the whole read, and no gapped alignment.
Hatem et al. BMC Bioinformatics 2013 14:184 doi:10.1186/1471-2105-14-184