Version Differences for HGAP
|
(→Hierarchical genome-assembly process)
|
(→Hierarchical genome-assembly process)
|
| Line 7: | |||
| - | '''Prepare for HGAP Protocol''' | + | '''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 setting minSubReadLength = 50, readScore = 0.75, minLength = 50 here ) | + | 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. |
| - | 3. smrtpipe.py --params=HGAP.xml xml:input.xml (~10hr for one data set) | + | 3. execute HGAP protocol. |
| + | smrtpipe.py --params=HGAP.xml xml:input.xml | ||
| Step 2 : Reference Import | Step 2 : Reference Import | ||