SAM (file format)

SAM (file format) is a text-based format for storing biological sequences aligned to a reference sequence developed by Heng Li. The acronym SAM stands for Sequence Alignment/Map. It is widely used for storing data, such as nucleotide sequences, generated by Next generation sequencing technologies.

The SAM format consists of a header and an alignment section. The binary representation of a SAM file is a BAM file, which is a compressed SAM file. SAM files can be analysed and edited with the software SAMtools.

See also

• FASTQ format
• List of file formats for molecular biology

References

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External links

• https://samtools.github.io/hts-specs/ detailed SAM format specification

• H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin: The Sequence Alignment/Map format and SAMtools. In: Bioinformatics. 25, 2009, S. 2078, doi:10.1093/bioinformatics/btp352.