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DOI: 10.1093/bioinformatics/btp352
OpenAccess: Green
This work has “Green” OA status. This means it may cost money to access on the publisher landing page, but there is a free copy in an OA repository.
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The Sequence Alignment/Map format and SAMtools

Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin

Computer science
Search engine indexing
Sequence alignment
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Li, H., Handsaker, B., Wysoker, A., Fennell, T. J., Ruan, J., Homer, N., Marth, G. T., Abecasis, G. R., & Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078.
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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.