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Curr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit 11.7. doi: 10.1002/0471250953.bi1107s32.

Aligning short sequencing reads with Bowtie.

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1
Johns Hopkins University, Baltimore, Maryland, USA.

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.

PMID:
21154709
PMCID:
PMC3010897
DOI:
10.1002/0471250953.bi1107s32
[Indexed for MEDLINE]
Free PMC Article
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