The Sequence Alignment/Map format and SAMtools

Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gábor Marth; Gonçalo R. Abecasis · Bioinformatics · 2009

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Author / responsible party

Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gábor Marth; Gonçalo R. Abecasis

Publisher

Bioinformatics

Year

2009

Language

English

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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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APA 7

Li, H, Handsaker, B, Wysoker, A, Fennell, T, Ruan, J, Homer, N, Marth, G, & Abecasis, G. R. (2009). The Sequence Alignment/Map format and SAMtools. https://doi.org/10.1093/bioinformatics/btp352

MLA

Li, Heng, et al. "The Sequence Alignment/Map format and SAMtools." 2009. https://doi.org/10.1093/bioinformatics/btp352.

Chicago

Li, Heng, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gábor Marth, and Gonçalo R. Abecasis. 2009. "The Sequence Alignment/Map format and SAMtools.". https://doi.org/10.1093/bioinformatics/btp352.

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Li, H. et al. 2009, The Sequence Alignment/Map format and SAMtools, Bioinformatics, available at: https://doi.org/10.1093/bioinformatics/btp352 [Accessed 9 Aug. 2026].

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Title: The Sequence Alignment/Map format and SAMtools

Author / contributors: Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gábor Marth; Gonçalo R. Abecasis

Publisher: Bioinformatics

Publication year: 2009

Language: English

Subjects

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Computer science; Search engine indexing; Sequence alignment; k-mer; Multiple sequence alignment; File format; Sanger sequencing; Sequence (biology); Alignment-free sequence analysis; Information retrieval; Computational biology; Genome