Journal Article

The Sequence Alignment/Map format and SAMtools

Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis and Richard Durbin

in Bioinformatics

Volume 25, issue 16, pages 2078-2079
Published in print August 2009 | ISSN: 1367-4803
Published online June 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp352

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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@sanger.ac.uk

Journal Article.  1276 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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