Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • long-range technologies for genome scaffolding

    Hi all,

    I am working on a mammalian genome project. We have an assembly from PacBio reads with N50 = 6.2 Mb. We would like to generate some long-range data that could be used for scaffolding. I am aware of several options, including Nanopore, Hi-C (with Dovetail or Phase Genomics), optical maps (Bionano), and synthetic long reads (10X). Can you share your experiences with these technologies? We need help choosing which one(s) to use.

    Thanks.

    Yury

  • #2
    You already have a good N50 with long reads. The options are combination of 10x Link reads, Hi-C and optical mapping. Searching " Vertebrate Genomes Project Plans to Combine Technologies for 'Near Gapless' Assemblies" should give more ideas but you might be asked to create an account to access it.

    Comment


    • #3
      Thanks for the tip, nucacidhunter!

      Comment


      • #4
        Scaffolding

        As nucacidhunter mentioned, I would highly recommend you work with the VGP group. I've work with the VGP and had excellent results for my de novo projects. They even do the hybrid assemblies!

        If your budget is tight, I would add HiC data from Phase Genomics or Arima Genomics. If phasing information is important, then add some 10X Genomics data (https://www.10xgenomics.com/solutions/assembly/).

        Comment

        Latest Articles

        Collapse

        • 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
        • seqadmin
          The Impact of AI in Genomic Medicine
          by seqadmin



          Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
          02-26-2024, 02:07 PM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 03-14-2024, 06:13 AM
        0 responses
        34 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-08-2024, 08:03 AM
        0 responses
        72 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-07-2024, 08:13 AM
        0 responses
        82 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-06-2024, 09:51 AM
        0 responses
        68 views
        0 likes
        Last Post seqadmin  
        Working...
        X