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The Sequence Alignment/Map format and SAMtools. | LitMetric
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The Sequence Alignment/Map format and SAMtools.

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

Bioinformatics

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.

Published: August 2009

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.

Download full-text PDF

 Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002PMC
http://dx.doi.org/10.1093/bioinformatics/btp352DOI Listing

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