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 9: | |||
| '''Prepare data for HGAP Protocol''' <br> | '''Prepare data for HGAP Protocol''' <br> | ||
| 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> | 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 : [[Media:HGAP.xml|HGAP.xml]]. we used default parameters setting mostly, and set minSubReadLength = 50, readScore = 0.75, minLength = 50. | + | 2. Build HGAP parameters XML file : [[Media:HGAP.xml|HGAP.xml]]. we used default parameters setting mostly, and set minSubReadLength = 50, readScore = 0.75, minLength = 50. <br> |
| 3. execute HGAP protocol. | 3. execute HGAP protocol. | ||
| smrtpipe.py --params=HGAP.xml xml:input.xml | smrtpipe.py --params=HGAP.xml xml:input.xml | ||