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SAM

136 bytes added, 13:30, 30 July 2010
What is SAM: refer to BamFile c++ library code
Most often it is generated as a human readable version of its sister [[BAM]] format, which stores the same data in a compressed, indexed, binary form.
Currently, most SAM format data is output from aligners that read FASTQ files and assign the sequences to a position with respect to a known reference genome. In the future, SAM will also be used to archive unaligned sequence data generated directly from sequencing machines.
The current definition of the format is at [[http://samtools.sourceforge.net/SAM1.pdf BAM/SAM Specification]].
If you are writing software to read SAM or BAM data, our C++ [[C++ Library: libbam|BamFile]] is a good resource to use.
== What Information is in SAM & BAM ==
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