title: The Sequence Alignment/Map format and SAMtools.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  http://samtools.sourceforge.net.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.
authors.forename: Heng
authors.initials: H
authors.lastname: Li
authors.forename: Bob
authors.initials: B
authors.lastname: Handsaker
authors.forename: Alec
authors.initials: A
authors.lastname: Wysoker
authors.forename: Tim
authors.initials: T
authors.lastname: Fennell
authors.forename: Jue
authors.initials: J
authors.lastname: Ruan
authors.forename: Nils
authors.initials: N
authors.lastname: Homer
authors.forename: Gabor
authors.initials: G
authors.lastname: Marth
authors.forename: Goncalo
authors.initials: G
authors.lastname: Abecasis
authors.forename: Richard
authors.initials: R
authors.lastname: Durbin
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D016678:Genome; D023281:Genomics; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software