Version Differences for HGAP
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(→Hierarchical genome-assembly process)
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(→Hierarchical genome-assembly process)
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| Line 8: | |||
| Step 1 : Prepare for HGAP Protocol | Step 1 : Prepare for HGAP Protocol | ||
| - | 1. Build input XML file (detail step please refer to the [https://github.com/PacificBiosciences/SMRT-Analysis/wiki/SMRT-Pipe-Reference-Guide-v2.0#PipeInputs tutorial]) | + | 1. Build input XML file (detail step please refer to the [https://github.com/PacificBiosciences/SMRT-Analysis/wiki/SMRT-Pipe-Reference-Guide-v2.0#PipeInputs tutorial]) <br> |
| - | 2. Build HGAP parameters XML file : HGAP protocal | + | 2. Build HGAP parameters XML file : [[Media:HGAP.xml|HGAP.xml]]. we used default parameter setting mostly, |
| [Note] : Please check the "minSubReadLength", "readScore", "minLength", Genome size (Setting minSubReadLength = 50, readScore = 0.75, minLength = 50 here ) | [Note] : Please check the "minSubReadLength", "readScore", "minLength", Genome size (Setting minSubReadLength = 50, readScore = 0.75, minLength = 50 here ) | ||
| 3. smrtpipe.py --params=HGAP.xml xml:input.xml (~10hr for one data set) | 3. smrtpipe.py --params=HGAP.xml xml:input.xml (~10hr for one data set) | ||