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  • Any de novo assembly software can produce ace file?

    I was used to edit the sequence in consed, so is there any software producing ace file for solexa data?
    I've tried Edena, it seems to obtain good assembly result, but having no ace files.

    thx.

  • #2
    Not that I know of. Now that I'm done fixing bugs (for the near future), I'll try and add this to euler-sr.

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    • #3
      I think abyss can produce ace files.

      At least the current version contains a perl script "abyss2ace" but I never tested it because it is not very well documented.

      Andreas

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      • #4
        abyss2ace

        abyss2ace isn't very well documented at the moment. I've add some Perl POD --help and --man options for the next release. The brief synopsis follows. To load the resulting ACE file in Consed, use

        consed -nophd -ace out.ace

        Cheers,
        Shaun

        SYNOPSIS
        KAligner -k K reads.fa contigs.fa >alignments.kalign
        abyss2ace reads.fa contigs.fa alignments.kalign >out.ace

        DESCRIPTION
        Create a Consed ACE assembly from an ABySS assembly. The reads are
        first aligned against the contigs using KAligner. These alignments are
        then converted to an ACE assembly.

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        • #5
          ABySS mailing list

          On the ABySS web page
          http://www.bcgsc.ca/platform/bioinfo/software/abyss

          there's a link (albeit not very conspicuous) to the mailing list:
          http://www.bcgsc.ca/mailman/listinfo/abyss-users

          Cheers,
          Shaun

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          • #6
            Great! THX a lot, everybody. I'll try as ur advice and feed back the result.

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            • #7
              Consed itself writes ACE files ..:

              addSolexaReads.perl will use cross_match to align reads against a given reference.
              Well, if you'd like to assemble denovo this does not work.

              Velvet does write AMOS afg files which can be converted into ACE ..

              cheers,
              Sven

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