title: Fast gapped-read alignment with Bowtie 2.
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.
authors.affiliation: Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, USA. blangmea@jhsph.edu
authors.forename: Ben
authors.initials: B
authors.lastname: Langmead
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods