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Bowtie

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Aligns short read geared toward mammalian re-sequencing. Bowtie is based on a Burrows-Wheeler index based on the full-text minute-space (FM) index. It follows two steps: an initial, ungapped seed-finding stage that derives advantage from the speed and memory efficiency of the full-text minute index and a gapped extension stage that employs dynamic programming and benefits from the efficiency of single-instruction multiple-data (SIMD) parallel processing available on modern processors.