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  • Increasing the length of the kmers od Spades beyond 127

    Hi,
    is there a way to increase the length of the kmers used by spades 3.5 beyond 127? Because I tried different kmers and I saw that the quality of the assembly is better with longer kmers.
    My reads are pretty long so I think it shouldn't be a problem to use bigger kmers.
    I have not much experience with spades, or with bioinformatics in general, so I hope my question is not woefully stupid.
    Thanks to everyone for the future answers

  • #2
    Bump

    I am facing the same issue as well and would like to know how to do this. Would it be similar to the way we increase it on velvet?

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    • #3
      You may specify the length of the kmers by adding " -k <int,int,...> " to default query "spades.py [options] -o <output_dir>".

      There is written in the manual:
      " Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128 and listed in ascending order). "

      Comment


      • #4
        Originally posted by Andrei D. View Post
        You may specify the length of the kmers by adding " -k <int,int,...> " to default query "spades.py [options] -o <output_dir>".

        There is written in the manual:
        " Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128 and listed in ascending order). "
        @ronaldrcutler wants to know (based on other threads posted here and on Biostars) if a value of more than 127 can be used in some way (clearly the software currently is limited at that level)?

        Are you from the group that developed SPAdes? If yes then can you provide an answer for that.

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        • #5
          No, I'm basically wet biologist from another group and don't know answer to this question.

          Comment


          • #6
            Originally posted by GenoMax View Post
            @ronaldrcutler wants to know (based on other threads posted here and on Biostars) if a value of more than 127 can be used in some way (clearly the software currently is limited at that level)?
            Yes this is exactly what I'm looking for since doing assemblies in other programs with a larger size yields better contigs and kmer size predictors also indicate that a high kmer should be at least tried.

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            • #7
              Originally posted by ronaldrcutler View Post
              Yes this is exactly what I'm looking for since doing assemblies in other programs with a larger size yields better contigs and kmer size predictors also indicate that a high kmer should be at least tried.
              Current limit is 127 with SPAdes unless you have programmatic chops to look in the source code to see if that can be changed.

              You can email SPAdes support with this question: spades.support at bioinf.spbau.ru

              Post their solution/answer here if you hear back.

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              • #8
                Any update on this?

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