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, 13:30, 30 July 2010
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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. |
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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. | + | 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. |
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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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| + | If you are writing software to read SAM or BAM data, our C++ [[C++ Library: libbam|BamFile]] is a good resource to use. |
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| == What Information is in SAM & BAM == | | == What Information is in SAM & BAM == |