SAM (file format)

<p>Sequence Alignment Map (SAM) is a text-based <a href="/facts/File_format/qrXbwJaH">format</a> originally for storing <a href="/facts/Sequence_alignment/p8GQfF7b">biological sequences aligned</a> to a <a href="/facts/RefSeq/5kBXXR8s">reference sequence</a> developed by <a href="/facts/Heng_Li/8sTjG8mg">Heng Li</a> and Bob Handsaker <i>et al</i>. It was developed when the <a href="/facts/1000_Genomes_Project/n8n8P60h">1000 Genomes Project</a> wanted to move away from the MAQ mapper format and decided to design a new format. The overall TAB-delimited flavour of the format came from an earlier format inspired by <a href="/facts/BLAT_(bioinformatics)/YCQPXFjI">BLAT</a>’s PSL. The name of SAM came from Gabor Marth from <a href="/facts/University_of_Utah/0lhlnv7c">University of Utah</a>, who originally had a format under the same name but with a different syntax more similar to a <a href="/facts/BLAST_(biotechnology)/uWufGxFH">BLAST</a> output. It is widely used for storing data, such as <a href="/facts/Nucleotide/pQKEwlJI">nucleotide</a> sequences, generated by <a href="/facts/Next_generation_sequencing/hsPsNCQW">next generation sequencing</a> technologies, and the standard has been broadened to include unmapped sequences. The format supports short and long reads (up to 128 Mbp) produced by different sequencing platforms and is used to hold mapped data within the Genome Analysis Toolkit (GATK) and across the <a href="/facts/Broad_Institute/RchJRWLN">Broad Institute</a>, the <a href="/facts/Wellcome_Sanger_Institute/uQchlx8p">Wellcome Sanger Institute</a>, and throughout the <a href="/facts/1000_Genomes_Project/n8n8P60h">1000 Genomes Project</a>.
</p>

SAM (file format) open-in-new

SAM (file format)