Table 1

Features supported by the tools
Bowtie Bowtie2 BWA SOAP2 MAQ RMAP GSNAP FANGS Novoalign mrFAST mrsFAST
Seed mm. Up to 3 Any Up to 2 Any Any
Non-seed mm. QS AS Count Count QS Count Count Count QS Count Count
Var. seed len. > 5 Any > 28
Mapping qual. Yes Yes Yes Yes
Gapped align. Yes Yes PE PE Yes Yes Yes Yes
Colorspace Yes Yes Yes Yes
Splicing Yes
SNP tolerance Yes
Bisulphite reads Yes Yes Yes Yes

PE: paired-end only, mm.: mismatches, QS: base quality score, count: total count of mismatches in the read, AS: alignment score, and empty cells mean not supported.

Hatem et al.

Hatem et al. BMC Bioinformatics 2013 14:184   doi:10.1186/1471-2105-14-184

Open Data