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<strong>Bowtie 2</strong> is an ultrafast and memory-efficient tool for aligning sequencing
reads to long reference sequences. It is particularly good at aligning reads of
about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian)
genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human
genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
gapped, local, and paired-end alignment modes.
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This research was supported in part by NIH grants R01-HG006102 and R01-GM083873 and AWS in Education research grants.
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