BWA

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Building a database

$ /path/to/bwa index <my fasta file>

Mapping

$ /path/to/bwa mem <db name> <fastq file> > <sam file>

See also

Project website - http://bio-bwa.sourceforge.net/
Manual - http://bio-bwa.sourceforge.net/bwa.shtml
References
- bwa-backtrack http://bioinformatics.oxfordjournals.org/content/25/14/1754
- bwa-sw http://bioinformatics.oxfordjournals.org/content/26/5/589
- fastmap (SNP calling) http://bioinformatics.oxfordjournals.org/content/28/14/1838

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