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  • Assembling raw reads with Canu, but without correction

    Hello friends,

    I have raw ONP and PacBio reads for the human genome, ecoli, and yeast, and I want to test Canu's performance on them, without correction.

    If I understand correctly, I would only execute the assemble step of Canu, and specify -nanopore-raw or -pacbio-raw, depending on the technology.

    Is this correct?

    Also, what other parameters should I set/tweak to get better accuracy in this scenario? Some candidate parameters I know:
    • rawErrorRate
    • utgOvlErrorRate
    • utgGraphDeviation
    • utgRepeatDeviation
    • utgRepeatConfusedBP


    Also, is there a platform where I can ask this to the developers of Canu? Is github/issues the right place for such a question?

    Any response greatly appreciated!
    Last edited by ekarais; 05-19-2019, 01:24 AM. Reason: Forgot to add something

  • #2
    Why not just specify -nanopore-corrected to probably make canu skip this stage ?

    Also, why would you even want to do this ? You'll get really awful results, the correction is there for a reason.

    Also, I think miniasm does rapid assembly on uncorrected reads, but then you have massive problems trying to correct base level errors in the asm afterwards.

    Comment


    • #3
      wtdbg2 will overlap long reads and then correct/consensus as a separate step (I know this doesn't help getting Canu to do it that way, just following up on colindaven's comment).

      Canu corrects reads before overlapping. I don't know if it can be shoe-horned into working on raw reads since it isn't expecting a 15% error rate when it overlaps. Just to offer additional annoyingly non-Canu advice, the flye assembler constructs an assembly graph before read correction.
      Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

      Comment

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