SAMtools is a widely-used software tool with comprehensive functionalities for post-processing read alignments in the Sequence Alignment/Map (SAM) format. The SAM format is a generic alignment format that allows storing read alignments against reference sequences, supporting short and long reads produced by different sequencing platforms up to 128 Mbp. SAMtools is a universal tool for processing read alignments, providing various utilities such as indexing, variant calling, and alignment viewing.

The SAM format is known for its flexibility in style, compact size, and efficiency in random access, making it the format of choice for alignments from the 1000 Genomes Project. By implementing these utilities, SAMtools allows researchers to easily process and analyze read alignments.


Bioinformatics;Mapping;Data architecture, analysis and design


  • Operation: Sequence assembly visualisation;Sequence alignment;Modelling and simulation;Formatting

  • Software interface: Suite

  • Language: C

  • License: The MIT/Expat License

  • Cost: Free

  • Version name: 1.17

  • Credit: Wellcome Trust, NIH Hapmap-1000 Genomes Project grant.

  • Input: SAM, FASTA

  • Output: SAM

  • Contact:

  • Collection: -

  • Maturity: Stable


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