Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • CLC genomics server for assembling large genomes

    Has anybody tried using CLCBio Genomics server for assembling large genomes (Panda, Human etc)?

    We have interest in assembling large genomes with small amount of RAM. Tried using CLCBio server based on their claims, but we were not able to do de novo assembly of panda (from Li et al Nat Gen 2010) and Human (from SRA) reads generated on Illumina platform.
    Our server configuration is 128 GB RAM and 2 Intel quad cores.
    We ran the assembly (both contig generation and mapping) with all default parameters.

    We would like to hear if anybody has had similar or maybe better experience.

  • #2
    I know some of my colleagues have had some success with the "CLCBio Assembly Cell" (or whatever their command line assembly tool is called) with plant genomes. Success meaning getting any useful contigs from a de novo assemblies, compared to most tools which needed too much RAM to do anything.

    Sorry I can't be more detailed.

    Comment


    • #3
      I was able to de novo assemble a 2GB genome pretty well with 24GB of RAM.

      Comment


      • #4
        Originally posted by NextGenSeq View Post
        I was able to de novo assemble a 2GB genome pretty well with 24GB of RAM.
        Can you please elaborate on this? What was the organism, how much data did you provide, the platform on which the data was generated, how long it took to complete the assembly etc. Greatly appreicate your response.

        Comment


        • #5
          It took a week with 350 million reads. Anymore than this you need more RAM. It's not published yet so can't say the organism besides it's vertebrate.

          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