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      Fast gapped-read alignment with Bowtie 2.

      Nature Methods

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          Abstract

          As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

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          Journal
          22388286
          3322381
          10.1038/nmeth.1923

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