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, 14:11, 26 February 2015
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| ==== Recommended Settings ==== | | ==== Recommended Settings ==== |
| | | |
− | By default, the alignment pipeline uses bwa aln. We recommend you use bwa mem instead. To use that, set in your configuration file:
| + | As of GotCloud version 1.16, the alignment pipeline uses <code>bwa mem</code> by default. Prior to version 1.16, the default aligner was <code>bwa aln</code>. |
| + | |
| + | You can override the defaults by setting in your configuration file: |
| + | * to use <code>bwa mem</code> (you do not need to set this in version 1.16 and later since it is the default) |
| MAP_TYPE = BWA_MEM | | MAP_TYPE = BWA_MEM |
− | | + | * to use <code>bwa aln</code> (you do not need to set this prior to version 1.16 since it is the default) |
| + | MAP_TYPE = BWA |
| | | |
| ==== Additional Required Settings ==== | | ==== Additional Required Settings ==== |