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 13: | |||
| smrtpipe.py --params=HGAP.xml xml:input.xml | smrtpipe.py --params=HGAP.xml xml:input.xml | ||
| - | '''Import reference''' | + | '''Import reference'''<br> |
| - | 1. After execute HGAP Protocol, there will be generating a polished_assemble.fasta.gz in "data" folder. Take it as reference. <br> | + | 1. After execute HGAP Protocol, there will be generating a polished_assemble.fasta.gz in "data" folder. The file serves as a reference for mapping the single pass reads as specified by the original filter parameters to the draft assembly to generate a higher accurate consensus sequence via Quiver <br> |
| 2. Import the reference by SMRT portal, because I don't konw how to import references by command line. <br> | 2. Import the reference by SMRT portal, because I don't konw how to import references by command line. <br> | ||
| 3. SMRT protal will generate a reference folder under /opt/smrtanalysis/common/userdata.d/references/XXXXXX. You can copy the whole folder to your working directory, or asign the path in the Quiver.xml <br> | 3. SMRT protal will generate a reference folder under /opt/smrtanalysis/common/userdata.d/references/XXXXXX. You can copy the whole folder to your working directory, or asign the path in the Quiver.xml <br> | ||