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, 11:10, 2 February 2017
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− | <br> '''K-tuple Alignment with Rapid Matching Algorithm''' | + | <!-- BANNER ACROSS TOP OF PAGE --> |
| + | {| style="width:100%; background:#ffb6c1; margin-top:1.2em; border:1px solid #ccc;" | |
| + | | style="width:100%; text-align:center; white-space:nowrap; color:#000;" | |
| + | <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KARMA is obsolete and not maintained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''' |
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| 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. |
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| = Download Karma = | | = Download Karma = |
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− | 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] |
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| = Build Karma = | | = Build Karma = |
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| = Optional flags = | | = Optional flags = |
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− | {| width="200" border="1" cellpadding="1" cellspacing="1" | + | Besides conforming to SAM specification, Karma developed its own optional tags to help evaluate mapping. |
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| + | {| cellspacing="1" cellpadding="1" border="1" style="width: 1034px; height: 291px;" |
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− | | XA | + | | XA |
| | Alignment PathTag | | | Alignment PathTag |
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− | | RG | + | | RG |
| | Sample GroupID | | | Sample GroupID |
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− | | HA | + | | HA |
| | numMatchContributors (possible hits checked by karma) | | | numMatchContributors (possible hits checked by karma) |
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− | | UQ | + | | UQ |
| | phred quality of this read, assuming it is mapped correctly | | | phred quality of this read, assuming it is mapped correctly |
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− | | NB | + | | NB |
| | Number of equally best hits | | | Number of equally best hits |
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− | | ER | + | | ER |
− | | Different kind of errors when mapping
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| + | Different kind of errors when mapping: |
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| + | 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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| |} | | |} |
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| + | <br> |
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| <br> | | <br> |
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| = Other test and check capabilities = | | = Other test and check capabilities = |
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| -s [int] -> set random number seed [12345] | | -s [int] -> set random number seed [12345] |
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− | = Karma File structure = | + | = Karma file structure = |
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| Upon successfully building references, you will obtain a list of reference files like below: | | Upon successfully building references, you will obtain a list of reference files like below: |
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− | {| style="width: 571px; height: 288px" border="1" cellspacing="1" cellpadding="1" width="571" | + | {| cellspacing="1" cellpadding="1" border="1" width="571" style="width: 571px; height: 288px;" |
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| <br> | | <br> |
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− | <br> | + | <br> |
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| = Karma TODO List = | | = Karma TODO List = |