Hello,
We just got SMRT Analysis installed in our lab and are trying to use HGAP for the first time. We have uploaded a SMRT cell into the portal and the HGAP protocol successfully runs, but the polished assembly contains only one single contig of 1200 bp of a 4.6 Mb genome.
I decided to tweak the parameters a bit and the next time I did the HGAP protocol, I returned a few more contigs. My question is this:
How do you determine the parameters of HGAP? I've sifted through the XML file provided by our sequencing facility, but it doesn't seem to have much information.
Any help you can give would be greatly appreciated!
-Alec
We just got SMRT Analysis installed in our lab and are trying to use HGAP for the first time. We have uploaded a SMRT cell into the portal and the HGAP protocol successfully runs, but the polished assembly contains only one single contig of 1200 bp of a 4.6 Mb genome.
I decided to tweak the parameters a bit and the next time I did the HGAP protocol, I returned a few more contigs. My question is this:
How do you determine the parameters of HGAP? I've sifted through the XML file provided by our sequencing facility, but it doesn't seem to have much information.
Any help you can give would be greatly appreciated!
-Alec
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