Unit

UNIT 11.7 Aligning Short Sequencing Reads with Bowtie

  1. Ben Langmead

Published Online: 1 DEC 2010

DOI: 10.1002/0471250953.bi1107s32

Lab Protocol Title

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

Additional Information

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

Keywords:

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