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- Jeff Barrick's introduction to NGS presentation
- Comparison of different aligners
- by Heng Li, developer of BWA and MAQ
- by Nils Homer, developer of BFAST
- Aligners
- bowtie (http://bowtie-bio.sourceforge.net/index.shtml) - very fast, not very sensitive
- BFAST wiki & manual - slow and relatively complicated, but tunable sensitivity
- bwa - fast, sensitive and easy to use
- bowtie2 - fast, sensitive, configurable, easy to use
- File formats
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