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.

Publication:
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]