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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.
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 genome. In the future, SAM will also be used to archive unaligned sequence data generated directly from sequencing machines.
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]].
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 ==
== What Information is in SAM & BAM ==
