Aligning Short Sequencing Reads with Bowtie

Ben Langmead1

1 Johns Hopkins University, Baltimore, Maryland
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 11.7
DOI:  10.1002/0471250953.bi1107s32
Online Posting Date:  December, 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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Table of Contents

  • Introduction
  • Basic Protocol 1: Aligning a Set of Short Reads to a Reference Genome
  • Alternate Protocol 1: Building an Index for a Set of Reference Sequences
  • Alternate Protocol 2: Alignment and Variation Detection Using Bowtie and SAMtools
  • Alternate Protocol 3: Running Bowtie with Various Command‐Line Options
  • Support Protocol 1: Obtaining and Installing the Bowtie Package
  • Support Protocol 2: Building Bowtie from Source
  • Support Protocol 3: Downloading and Installing a Prebuilt Bowtie Index
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

   Burrows, M. and Wheeler, D.J. 1994. A block sorting lossless data compression algorithm. Technical Report 124. Digital Equipment Corporation, Palo Alto, Calif.
   Cock, P.J., Fields, C.J., Goto, N., Heuer, M.L., and Rice, P.M. 2010. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 38:1767‐1771.
   Ferragina, P. and Manzini, G. 2000. Opportunistic data structures with applications. In Proceedings of the 41st Annual Symposium on Foundations of Computer Science. IEEE Computer Society.
   Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. 2009. Ultrafast and memory‐efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25.
   Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078‐2079.
Key Reference
   Langmead et al., 2009. See above.
  Describes the indexing technique underlying the tool and compares to other alignment tools.
Internet Resource
  http://bowtie‐bio.sf.net
  The project's home page where the latest version of the package can be downloaded and where announcements are made.
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