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, 16:30, 29 July 2010
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| == What is SAM == | | == What is SAM == |
− | The '''SAM Format''' is a text format for storing aligned reads in a series of tab delimited ASCII columns. | + | The '''SAM Format''' is a text format for storing sequence data in a series of tab delimited ASCII columns. |
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− | Most often it is generated as a human readable projection of its sister [[BAM]] format, which can store data in a compact, indexed, binary representation. | + | 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. |
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| + | 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. |
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| 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]]. |
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| == What Information is in SAM & BAM == | | == What Information is in SAM & BAM == |