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lh3 committed May 25, 2013
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Expand Up @@ -20,7 +20,7 @@ Illumina reads.

For all the algorithms, BWA first needs to construct the FM-index for the
reference genome (the **index** command). Alignment algorithms are invoked with
different sub-commands: **aln**/**samse**/**sampe** for BWA-backtrack,
different sub-commands: **aln/samse/sampe** for BWA-backtrack,
**bwasw** for BWA-SW and **mem** for the BWA-MEM algorithm.

###Availability
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