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Bowtie is an ultrafast, memory-efficient short read alner geared toward quickly alning large sets of short DNA sequences (reads) to large genomes.

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Bowtie can also output alnments in the standard SAM format, allowing Bowtie to interoperate with other tools supporting SAM, including the SAools consensus, SNP, and indel ers.

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Multiple processors can be used simultaneously to achieve greater alnment speed.

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It alns 35-base-pair reads to the human genome at a rate of 25 million reads per hour on a typical workstation.

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