Table 2.
Bisulfite Read mapping tools evaluated in this survey, listed by their mapping and indexing strategy.
| Mapper name | Strategy | Indexing | Version | Citations |
|---|---|---|---|---|
| Bismark | 3 letter | BWT (bowtie 2/bowtie 1) | 0.19.1 | 1.176 |
| BSMAP | wild-card | Hash table (SOAP) | 2.73 | 3 |
| BS-Seeker2 | 3 letter | BWT (bowtie 2) | 2.1.5 | 135 |
| Bwa-meth | 3 letter | BWA mem | 0.2.2 | 3 |
| GEM3 | 3 letter | Custom FM index | 3.6.1-2 | 236 |
| GSNAP | wild-card | Hash table | 2019-06-10 | 83 |
| Segemehl | wild-card | Enhanced suffix array | 0.2.0 | 283 |
The number of citations is based on the Web of Science Core Collection (date: 19.1.2020).