UNIT 11.7 Aligning Short Sequencing Reads with Bowtie

  1. Ben Langmead

Published Online: 1 DEC 2010

DOI: 10.1002/0471250953.bi1107s32

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Langmead, B. 2010. Aligning Short Sequencing Reads with Bowtie. Current Protocols in Bioinformatics. 32:11.7:11.7.1–11.7.14.

Author Information

  1. Johns Hopkins University, Baltimore, Maryland

Publication History

  1. Published Online: 1 DEC 2010
  2. Published Print: DEC 2010


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. Curr. Protoc. Bioinform. 32:11.7.1-11.7.14. © 2010 by John Wiley & Sons, Inc.


  • short reads;
  • read alignment;
  • alignment;
  • read mapping;
  • mapping;
  • genome indexing;
  • comparative genomics;
  • software package