The 1000 Genomes Project has used several different alignment algorithms during its duration:
| Project stage | Sequencing technology | Alignment algorithm |
|---|---|---|
| Pilot | Illumina | MAQ |
| Pilot | SOLiD | Corona lite |
| Pilot | 454 | ssaha |
| Main | Illumina | BWA |
| Main | SOLiD | BFAST |
| Main | 454 | ssaha (first set) |
| Main | 454 | smalt (final set) |
The full process is described in the README