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Fast gapped-read alignment with Bowtie 2

Ben Langmead Steven L Salzberg.
Nat Methods.. 2012 Mar 4;9(4):357-359.
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.