The Sequence Alignment/Map format and SAMtools

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Abstract

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.

Availability: http://samtools.sourceforge.net

Contact: rd@ 123456sanger.ac.uk

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Author and article information

Journal

Journal ID (nlm-ta): Bioinformatics

Journal ID (publisher-id): bioinformatics

Journal ID (hwp): bioinfo

Title: Bioinformatics

Publisher: Oxford University Press

ISSN (Print): 1367-4803

ISSN (Electronic): 1460-2059

Publication date (Print): 15 August 2009

Publication date (Electronic): 8 June 2009

Publication date PMC-release: 8 June 2009

Volume: 25

Issue: 16

Pages: 2078-2079

Affiliations

¹ Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, ²Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA, ³Beijing Institute of Genomics, Chinese Academy of Science, Beijing 100029, China, ⁴Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, ⁵Department of Biology, Boston College, Chestnut Hill, MA 02467, ⁶Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA and ⁷ http://1000genomes.org

Author notes

^*To whom correspondence should be addressed.

^†The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.

Associate Editor: Alfonso Valencia

Article

Publisher ID: btp352

DOI: 10.1093/bioinformatics/btp352

PMC ID: 2723002

PubMed ID: 19505943

SO-VID: 96b7bc64-d0fc-44a2-9a95-f1a765358bc6

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

History

Date received : 28 April 2009

Date revision received : 28 May 2009

Date accepted : 30 May 2009

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