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; 1000 Genome Project Data Processing Subgroup

doi:10.1093/bioinformatics/btp352

The Sequence Alignment/Map format and SAMtools

Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8.

Authors

Heng Li¹, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin; 1000 Genome Project Data Processing Subgroup

Affiliation

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

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Base Sequence
Computational Biology / methods*
Genome
Genomics
Molecular Sequence Data
Sequence Alignment / methods*
Sequence Analysis, DNA / methods*
Software*

Abstract

Publication types

MeSH terms

Grants and funding