The Sequence Alignment/Map Format and SAMtools

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2009 Jun 10

PMID 19505943

Citations 30476

Authors

Heng Li

Bob Handsaker

Alec Wysoker

Tim Fennell

Jue Ruan

Nils Homer

Gabor Marth

Goncalo Abecasis

Richard Durbin

Affiliations

Soon will be listed here.

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.

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