The Sequence Alignment/Map format and SAMtools

Abstract

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@sanger.ac.uk

Keywords

Computer scienceSearch engine indexingSequence alignmentk-merMultiple sequence alignmentFile formatSanger sequencingSequence (biology)Alignment-free sequence analysisInformation retrievalComputational biologyGenomeDNA sequencingDatabaseBiologyGeneticsPeptide sequenceDNAGene

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Publication Info

Year: 2009
Type: article
Volume: 25
Issue: 16
Pages: 2078-2079
Citations: 63241
Access: Closed

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APA Style

                            
                                
                                    Heng Li, 
                                
                                    Robert E. Handsaker, 
                                
                                    Alec Wysoker
                                
                                et al.
                            
                            (2009). 
                            The Sequence Alignment/Map format and SAMtools. 
                            Bioinformatics
                            , 25
                            (16)
                            , 2078-2079.
                            https://doi.org/10.1093/bioinformatics/btp352
                        

Identifiers

DOI: 10.1093/bioinformatics/btp352