Aligning short sequencing reads with Bowtie.

Current protocols in bioinformatics ·Vol. Chapter 11 ·2010-12-00 ·Pages Unit 11.7

Langmead B

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.

MeSH Terms

Algorithms Consensus Sequence Genome Genomics/methods Sequence Alignment/methods Sequence Analysis, DNA/methods Software

Authors & Affiliations

1 authors, click to expand affiliations / ORCID

Langmead Ben

Johns Hopkins University, Baltimore, Maryland, USA.

References (2)

2 references, click to expand

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Genome Biol. 2009;10(3):R25 PMID: 19261174
The Sequence Alignment/Map format and SAMtools.
Bioinformatics. 2009 Aug 15;25(16):2078-9 PMID: 19505943

Article Info

Journal

Current protocols in bioinformatics

Abbr.

Curr Protoc Bioinformatics

ISSN

1934-340X

DOI

10.1002/0471250953.bi1107s32

Published

2010-12-00

Pages

Unit 11.7

Language

English

Region

United States

NLM ID

101157830

PMCID

PMC3010897

Subset

Grants

NIGMS NIH HHS · R01 GM083873 · United States

NHGRI NIH HHS · R01 HG006102 · United States

NHGRI NIH HHS · P41 HG004059 · United States

NHGRI NIH HHS · R01 HG005220-02 · United States

NHGRI NIH HHS · P41 HG004059-05 · United States

NLM NIH HHS · R01 LM006845-10 · United States

NLM NIH HHS · R01 LM006845 · United States

NHGRI NIH HHS · R01 HG005220 · United States

External Links

PubMed source DOI: 10.1002/0471250953.bi1107s32 PMC Full Text

Analysis Services

Aligning short sequencing reads with Bowtie.

Contact

WeChat Official Account