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  • Memory-efficient reference-based assembly / or any Velvet versions online?

    I am trying to do something very simple here, but due to memory limitations I am stuck, and can no longer use Velvet's Columbus feature.

    I had the reads from a shotgun sequencing of a bacteria.
    I performed genome assembly using velvet (kmer size 31) and received the contigs

    Now I want to perform assembly once again on those reads, but this time, reference-based assembly, using those Velvet contigs as reference.

    How can I do that in an easy way?

    What I tried to do was this: using BWA to index the contigs, align the contigs with my reads and then using bwa sampe to get the aligned sam file. Sorted the sam file. used velveth with -reference option on the contigs file and -sam on the sorted sam file, and I received a Segmentation Fault (core dumped) error... Which as far as I have searched for, is related to memory.. Since this is an urgent task and I need to finish it soon. I wonder whether there are any other ways to do reference-based assembly or is there an online version of Velvet? I tried some on galaxy sites, but none offered the -reference option.

  • #2
    There are other ways to do reference-guided assembly, but it does not really make any sense to me why you would want to do it in this case. Mapping paired reads to an assembly and scaffolding with a standalone tool like SSPACE might be useful, though.

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    • #3
      Bowtie2 would perform a similar task but I'm not sure if it's less computationally heavy. I usually find it is quicker too.

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