title: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
abstract: Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source (http://bowtie.cbcb.umd.edu).
authors.affiliation: Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA. langmead@cs.umd.edu
authors.forename: Ben
authors.initials: B
authors.lastname: Langmead
authors.forename: Cole
authors.initials: C
authors.lastname: Trapnell
authors.forename: Mihai
authors.initials: M
authors.lastname: Pop
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*