SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that:

  • Is flexible enough to store all the alignment information generated by various alignment programs;
  • Is simple enough to be easily generated by alignment programs or converted from existing alignment formats;
  • Is compact in file size;
  • Allows most of operations on the alignment to work on a stream without loading the whole alignment into memory;
  • Allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus.

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.


Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]

Companion Programs: