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  • sklages
    replied
    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

    Leave a comment:


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

    Leave a comment:


  • sjackman
    replied
    ABySS mailing list

    On the ABySS web page
    Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler


    there's a link (albeit not very conspicuous) to the mailing list:


    Cheers,
    Shaun

    Leave a comment:


  • sjackman
    replied
    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.

    Leave a comment:


  • andpet
    replied
    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

    Leave a comment:


  • mchaisso
    replied
    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.

    Leave a comment:


  • fusu
    started a topic Any de novo assembly software can produce ace file?

    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.

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