Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.

    Comment


    • #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

      Comment


      • #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.

        Comment


        • #5
          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

          Comment


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

            Comment


            • #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

              Comment

              Latest Articles

              Collapse

              • seqadmin
                Strategies for Sequencing Challenging Samples
                by seqadmin


                Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                03-22-2024, 06:39 AM
              • seqadmin
                Techniques and Challenges in Conservation Genomics
                by seqadmin



                The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                Avian Conservation
                Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                03-08-2024, 10:41 AM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, Yesterday, 06:37 PM
              0 responses
              8 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, Yesterday, 06:07 PM
              0 responses
              8 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-22-2024, 10:03 AM
              0 responses
              49 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-21-2024, 07:32 AM
              0 responses
              67 views
              0 likes
              Last Post seqadmin  
              Working...
              X