Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Pacbio assembly of polymorphic genome

    Hi guys,

    a quick question. I am new to pacbio. I've just received pacbio data for assembling a genome (low coverage). It comes from a highly polymorphic genome. What is the most suitable assembler that would handle pacbio and that would let me also keep the two haplotypes separeted?

    Best regards,

    Carlos

  • #2
    Originally posted by carlos View Post
    Hi guys,

    a quick question. I am new to pacbio. I've just received pacbio data for assembling a genome (low coverage). It comes from a highly polymorphic genome. What is the most suitable assembler that would handle pacbio and that would let me also keep the two haplotypes separeted?

    Best regards,

    Carlos
    With low coverage data, you will barely be able to assemble a decent un-separated (haploid) assembly. Typically we recommend about 60X coverage for haploid assembly, and twice that for diploid assembly, or else won't have enough coverage to sufficiently resolve both haplotypes

    What does "Low coverage" equate to?

    That said, FALCON or Canu are your best options at this point.
    Last edited by gconcepcion; 10-28-2016, 08:10 AM.

    Comment


    • #3
      Originally posted by gconcepcion View Post
      With low coverage data, you will barely be able to assemble a decent un-separated (haploid) assembly. Typically we recommend about 60X coverage for haploid assembly, and twice that for diploid assembly, or else won't have enough coverage to sufficiently resolve both haplotypes

      What does "Low coverage" equate to?

      That said, FALCON or Canu are your best options at this point.
      Hi,

      10X, I wanted to say to help the assembly (scaffolding instead of denovo). I would like to use it for scaffolding in a diploid way.

      Regards

      Comment


      • #4
        Originally posted by carlos View Post
        Hi,

        10X, I wanted to say to help the assembly (scaffolding instead of denovo). I would like to use it for scaffolding in a diploid way.

        Regards
        If you can shed some light on what you are trying to do, and what data you have to start with, it will make it easier for people to help you.

        Now I understand that you are trying to scaffold short read data, and not perform Denovo assembly of low coverage pacbio data alone. How much short read data do you have? How large is the genome? What evidence do you have that the genome is highly polymorphic? Do you already have a short read assembly? How does it look?

        To my knowledge, there are no current tools available for scaffolding short read assemblies with (extremely) low coverage pacbio data resulting in diploid assemblies.

        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
        11 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        51 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