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SMRT Link 7.0 - HGAP

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  • 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

  • #2
    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.
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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    • #3
      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

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      • #4
        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.
        Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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        • #5
          Well, finally got version 8 installed. It never completes, just hangs forever. Seems like a terrible assembler.

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          • #6
            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

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            • #7
              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.

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