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<br> '''K-tuple Alignment with Rapid Matching Algorithm'''
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<div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">KARMA is obsolete and not maintained</div>
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'''K-tuple Alignment with Rapid Matching Algorithm'''
Karma uses an existing reference to align short reads, such as those generated by Illumina sequencers.
Karma uses an existing reference to align short reads, such as those generated by Illumina sequencers.
= Download Karma =
= Download Karma =
To get a copy go to [http://www.sph.umich.edu/csg/pha/karma/download/ Karma Download]
To get a copy go to [http://csg.sph.umich.edu//pha/karma/download/ Karma Download]
= Build Karma =
= Build Karma =
Besides conforming to SAM specification, Karma developed its own optional tags to help evaluate mapping.
Besides conforming to SAM specification, Karma developed its own optional tags to help evaluate mapping.
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| XA
| XA
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| ER
| ER
| Different kind of errors when mapping
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Different kind of errors when mapping:
ER:Z:no_match -> UNSET_QUALITY<br>ER:Z:invalid_bases -> INVALID_DATA (not used yet)<br>ER:Z:duplicates -> EARLYSTOP_DUPLICATES ( early stop due to reaching max number of best matches, with all bases matched)<br>ER:Z:quality -> EARLYSTOP_QUALITY (early stop due to reaching max posterior quality)<br>ER:Z:repeats -> REPEAT_QUALITY (not used yet)<br>
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= Other test and check capabilities =
= Other test and check capabilities =
