Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Oases assembly merge times out on a cluster

    Hi,

    I have run velvet-oases on k-mers 21 thru 55, and I am trying to merge the assemblies now. I tried using the velveth --> velvetg --> oases approach from the "Assembly Merging" section of the manual, but velvetg runs for an abnormally long duration (>48 hours), and the cluster on which I'm running the script times out.

    I have tried providing 244 GB of RAM, but it makes no difference - the "Log" file from velveth is written to once when the script starts running, and no other file(including the redirected stderr/stdout) is touched for the entire duration of the run.

    Any idea how I could tackle this?

    --
    Thanks,
    Ram
    Ram

  • #2
    Small K-mer assemblies are pretty computationally heavy. How many reads are you working with? Have you done any quality filtering on your reads?

    If you are using a massive amount of reads, you may want to consider implementing some sort of digital normalization (Trinity can do this independent of assembly and Titus Brown has a version of digital normalization as well http://arxiv.org/abs/1203.4802).

    Reducing reads and reads with errors will greatly reduce memory and run time.

    Comment


    • #3
      Hi,

      Thank you so much for the response!

      I'm working with Titus Brown's version of digital normalization right now - that brought the reads down from around 289 mil to 12 mil (6X2) PE reads and 7 mil SE reads (after a strip-and-split ).

      I asked my sequencing provider - the only QC step was the pass filter run on raw reads. Is there a specific QC filter I can use for transcriptome reads?



      Originally posted by jgibbons1 View Post
      Small K-mer assemblies are pretty computationally heavy. How many reads are you working with? Have you done any quality filtering on your reads?

      If you are using a massive amount of reads, you may want to consider implementing some sort of digital normalization (Trinity can do this independent of assembly and Titus Brown has a version of digital normalization as well http://arxiv.org/abs/1203.4802).

      Reducing reads and reads with errors will greatly reduce memory and run time.
      Ram

      Comment


      • #4
        No problem.

        One thing you may want to try BEFORE digital normalization is trimming reads based on quality score. There are quite a few pieces of software that can do this (trimmomatic and trim galore to name a couple).

        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