Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • de novo assembly of polyploid genomes?

    Hi there,

    looking for feedback on the performance of different assembly tools used for
    polyploid genomes, based on 454 data, especially concerning assembly quality.

    gsAssembler has a 'heterozygoteMode', but I'm unsure how well it works. Any
    other tools you've used or can comment on?

  • #2
    The same question. Any comments?

    Comment


    • #3
      Originally posted by pengchy View Post
      The same question. Any comments?
      There's not a lot positive to say, unfortunately.

      It is inherently difficult to assemble a complete homozygous genome using next gen data, diploid is harder still, and polyploid genomes even worse. AFAIK, such genomes are currently done using pre-separation of chromosomes in the lab.

      Even in theory, the amount of data needed to disambiguate the various near-identical sequences into individual chromosome variants of a polyploid is massive.

      First, you need enough reads to get a connected graph which includes all variants of the chromosome (and allows you to clean up errors vs variants). Then you enough long paired-end / mate pair data to find several unambiguous routes through the graph, with each route well supported by unique sets of spanning pairs of reads at every branching point. And this is all on top of all the ambiguity which comes from repeats and near repeats within each chromosome.

      And i doubt that any tool out there today is really optimized for this purpose.

      Net result - this is really hard to do.

      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, 03-27-2024, 06:37 PM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-27-2024, 06:07 PM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      53 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      69 views
      0 likes
      Last Post seqadmin  
      Working...
      X