title: Aligning short sequencing reads with Bowtie.
abstract: This unit shows how to use the Bowtie package to align short sequencing reads, such as those output by second-generation sequencing instruments. It also includes protocols for building a genome index and calling consensus sequences from Bowtie alignments using SAMtools.
authors.affiliation: Johns Hopkins University, Baltimore, Maryland, USA.
authors.forename: Ben
authors.initials: B
authors.lastname: Langmead
mesh_terms: D000465:Algorithms; D016384:Consensus Sequence; D016678:Genome; D023281:Genomics / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software