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  • cement_head
    replied
    Originally posted by lilou View Post
    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.

    Leave a comment:


  • lilou
    replied
    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

    Leave a comment:


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

    Leave a comment:


  • SNPsaurus
    replied
    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.

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  • cement_head
    replied
    Originally posted by SNPsaurus View Post
    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.
    Last edited by cement_head; 10-06-2019, 06:10 AM. Reason: clarification

    Leave a comment:


  • SNPsaurus
    replied
    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.

    Leave a comment:


  • cement_head
    started a topic SMRT Link 7.0 - HGAP

    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?

    ---------------------------------------------------------------------

    My mistake - a corrupted downloaded data file was the culprit; should have checked the mdm5 checksum before starting!
    Last edited by cement_head; 10-06-2019, 06:12 AM. Reason: correction

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