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Maq, BWA, and Bowtie Compared

MAQ, BWA, BOWTIE were compared for purposes of variant detection. Summary: BOWTIE is slightly more sensitive than BWA or MAQ. MAQ is an order of magnitude slower than the BWT-based aligners. BWA and BOWTIE are basically comparable.

http://bits-ngs.blogspot.com/2009/08/maq-bwa-and-bowtie-compared.html

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