Table 3. Characteristics of several popular open-source/binary NGS aligners.
| Software | Sequencing platform | Ability to perform gapped alignment | Quality awareness | Ability to align PE reads | Reference |
|---|---|---|---|---|---|
| BFAST | I,4 | + | − | + | Homer et al. (2009) |
| Bowtie | I,4,Sa | − | + | + | Langmead et al. (2009) |
| Bowtie 2 | I,4,Ion | + | + | + | Langmead and Salzberg (2012) |
| BWA | I,4,Sa | + | + | + | Li and Durbin (2009) |
| CloudBurst | non-specific | + | − | − | Schatz (2009) |
| GSNAP | I,4,Sa,Ion | + | − | + | Wu and Nacu (2010) |
| MAQ | I | − | + | + | Li et al. (2008) |
| MOSAIK | I,4,Sa,Ion | + | + | + | NA |
| mrFAST | I | − | + | + | Alkan et al. (2009) |
| mrsFAST | I | − | + | + | Hach et al. (2010) |
| NextGenMap | I,4,Ion | + | − | + | Sedlazeck et al. (2013) |
| PASS | I,4 | + | + | + | Campagna et al. (2009) |
| RazerS | I,4 | + | − | + | Weese et al. (2009) |
| segemehl | I,4,Sa,Ion | + | − | + | Hoffmann et al. (2009) |
| SHRiMP | I,4 | + | − | + | Rumble et al. (2009) |
| SHRiMP 2 | I,4 | − | + | + | David et al. (2011) |
| SOAP2 | I | + | − | + | Li et al. (2009b) |
| Stampy | I | + | + | + | Lunter and Goodson (2011) |
Abbreviations: I, Illumina; Ion, Ion Torrent; NA, no publication available; NGS, next-generation sequencing; PE, paired end; Sa, ABI Sanger; 4, Roche 454.
Information obtained from http://www.ebi.ac.uk/~nf/hts_mappers/ (last accessed August 2016). Popularity was assessed by the number of citations of the software.