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  • Close bacterial draft genome with other draft genome

    Hi,

    I would like to reduce contig number of the bacterial draft genome I'm trying to close. The draft genome is in 47 contigs and has been assembled by me, using Phred, Phrap, Consed.

    I'm thinking in using the other draft genome that has been published (same bacterial specie) perform this task.

    Do you think I should start from zero, that is, join the not assembled raw data of the two drafts published and see what happens, or use a tool having as input the two assembled drafts?

    Thanks for you help, Bernardo

    P.S. I also posted in Biostar this question.

  • #2
    The Quest for Completion

    The problem with doing this is that it basically assumes that the genomes are colinear. They may be, or may not. Should they not be colinear, the areas of 'assisted' assembly are likely in spots which are the most problematic - genomic islands, duplication and amplification, repetitive, insertion sequences, mobile elements, etc.

    There has been the idea of gene-assisted assembly, but this isn't typically for finishing the final 40 gaps. You are probably past that point.

    Also, be wary, your existing contigs may be 'over assembled' already.

    The tools that can best help you at this point are long read data, optical maps, hybridization data, Sanger walking, and the like.

    Thank you for seeking to close the genome and best of luck.

    Comment


    • #3
      With the caveats as mentioned by @bckirkup, you could try Mauve Contig Mover for this.

      Comment

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