Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • parallel de novo assembler

    Hi,

    I'm interested in using a parallel assembler for de novo assembler right now. I know that Abyss can use MPI and SOAPdenovo is multi-threaded. However, the machines available to me currently don't support MPI and SOAPdenovo is very hard to use without any useful docs. Can someone provide me with some more information on this topic? Thanks! :-)

  • #2
    Sylvain Forêt and Daniel Zerbino are working on a parallel version of Velvet that should be available soon. Velvet works really well for de novo assembly, and if you are working with transcriptome data, try the multiple-k method (http://genome.cshlp.org/content/20/10/1432.full)

    Comment


    • #3
      Is there any more to this? I saw a publication recently showing an MPI adaptation to velvet, but the source was not published, and there is no mention of it on the Velvet website.

      Comment


      • #4
        Hi,
        This could be of your interest http://seqanswers.com/forums/showthr...&highlight=Ray.
        Thanks,
        Rahul
        Rahul Sharma,
        Ph.D
        Frankfurt am Main, Germany

        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
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        9 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        50 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