Aligning short sequencing reads with Bowtie

Ben Langmead

Research output: Contribution to journalArticlepeer-review

578 Scopus citations


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.

Original languageEnglish (US)
Article number11.7
JournalCurrent Protocols in Bioinformatics
Issue numberSUPP.32
StatePublished - Dec 2010
Externally publishedYes


  • Alignment
  • Comparative genomics
  • Genome indexing
  • Mapping
  • Read alignment
  • Read mapping
  • Short reads
  • Software package

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry


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