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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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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 runs on the command line under Windows, Mac OS X, Linux, and Solaris.

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

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