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-   -   SMRT Link 7.0 - HGAP (http://seqanswers.com/forums/showthread.php?t=91169)

cement_head 10-03-2019 01:54 PM

SMRT Link 7.0 - HGAP
 
Has anyone gotten the HGAP assembler to work? It seems that it just barfs at different places constantly. Doesn't seem to be very robust at all.

I've used CANU before, so I'm going to try to go back to that...

What about the wtdbg2assembler?

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My mistake - a corrupted downloaded data file was the culprit; should have checked the mdm5 checksum before starting!

SNPsaurus 10-03-2019 02:34 PM

What kind of genome are you trying to assemble? I usually go with flye as a first pass (fast, memory efficient) and then Canu if flye underperforms (they seem to trade off which gives a better assembly in our hands). wtdbg2 is fun to try a quick check but I don't think it is as feature complete as flye or canu.

cement_head 10-06-2019 07:09 AM

Quote:

Originally Posted by SNPsaurus (Post 228717)
What kind of genome are you trying to assemble? I usually go with flye as a first pass (fast, memory efficient) and then Canu if flye underperforms (they seem to trade off which gives a better assembly in our hands). wtdbg2 is fun to try a quick check but I don't think it is as feature complete as flye or canu.

Well, figured it out - was a corrupted file from the download!

Wood Frog Genome - 6 Gbp

Got it working, but it barfs as it wants to fo a 30x coverage and from the RAW reads, it comes up a few thousand short. Would the SEED COVERAGE parameter (in the Advanced tab) be the one I would want to change? From say 30 to 25? (Just to get a rough assembly?) I'm waiting on HiSeq data to do a combined ONT + Pac Bio + HiSeq assembly in CANU.

SNPsaurus 10-06-2019 10:08 AM

Oh my, that's a big one. How much memory is it using?

If you just want a rough assembly, I would do wtdbg2 as you can get a sense of contig lengths without consensus generation. I've done flye with 10X read coverage (to look at how much is chloroplast and bacteria in a dirty sample) and it didn't protest. Sorry, haven't used HGAP.

cement_head 11-19-2019 05:45 AM

Well, finally got version 8 installed. It never completes, just hangs forever. Seems like a terrible assembler.

lilou 11-22-2019 11:35 AM

Hello
HGAP does not support this size of genome. It is made for <=3Gb genomes.
Best to use Falcon which is also a diploid aware assembler

cement_head 12-04-2019 07:56 PM

Quote:

Originally Posted by lilou (Post 229579)
Hello
HGAP does not support this size of genome. It is made for <=3Gb genomes.
Best to use Falcon which is also a diploid aware assembler

Interesting. HGAP4 Manual doesn't mention this, but the FALCON GitHub repo does - the impression that SMRTLink software gives is that it is a GUI wrapper for FALCON. I guess not. Thanks.


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