Version Differences for HGAP
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(→Hierarchical genome-assembly process)
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(→Hierarchical genome-assembly process)
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| =Hierarchical genome-assembly process= | =Hierarchical genome-assembly process= | ||
| - | We downloaded smrtanalysis-2.0.1 from [http://pacificbiosciences.github.io/DevNet/ DevNet], and executed the [[Media:HGAP.xml | RS_HGAP_Assembly.1]] and [[Media:Quiver.xml | RS_Modification_and_Motif_Analysis.1]] protocol. | + | We downloaded smrtanalysis-2.0.1 from [http://pacificbiosciences.github.io/DevNet/ DevNet], you can run the RS_HGAP_Assembly.1 and RS_Modification_and_Motif_Analysis.1 protocols on SMRT Portal or execute by command line. |
| + | 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]) | ||
| + | 2. Build HGAP parameters XML file : HGAP protocal | ||
| + | [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) | ||
| + | Step 2 : Reference Import | ||
| + | 1. After execute HGAP Protocol, there will be generating a polished_assemble.fasta.gz in "data" folder. Take it as reference. | ||
| + | 2. Import the reference by SMRT portal, because I don't konw how to import references by command line. | ||
| + | 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 | ||
| + | Step 3 : Prepare for Quiver | ||
| + | 1. Build Quiver parameters XML file : Quiver protocal | ||
| + | [Note] : Please check the "minSubReadLength", "readScore", "minLength", Reference file folder path. (Setting minSubReadLength = 50, readScore = 0.75, minLength = 50 here ) | ||
| + | 2. smrtpipe.py --params=Quiver.xml xml:input.xml | ||
| + | and executed the [[Media:HGAP.xml | RS_HGAP_Assembly.1]] and [[Media:Quiver.xml | RS_Modification_and_Motif_Analysis.1]] protocol. | ||