Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • best way to close gaps in genome with single reads

    What is the best way to close gaps (stretches of Ns) in a genome with single reads and also combine contigs/scaffolds.

  • #2
    Get more sequencing done.

    It may even be cost effective in some cases to design primers and use "Sanger" capillary sequencing to target theses specific gaps or confirm particular contig junctions.

    If you're doing more high throughput, I'd consider a paired end library - using a different insert length if you've already got some paired end data.

    Comment


    • #3
      I actually meant in silico since I have a draft genome and additional single reads already. I thought of using velvet, the contigs from the draft genome as long reads and add the reads I have in addition, but was wondering whether there are any other (better) ideas out there. Thanks in advance for any suggestion.

      Comment


      • #4
        Difficult. You really want paired end reads. (Very) long reads, eg Pac Bio, would be useful too.

        There are a already a number of threads on this site about genome assembly strategies.

        One suggestion - create contig sets from original reads, then new reads separately eg Velvet.
        Trim to 1999bp.
        Input into Newbler.

        Comment


        • #5
          Have you tried GapCloser from the SOAP package? I could close/remove ~80% of the Ns in a 1Gb draft assembly by using paired end reads with inserts of 200-500bp.

          Of course, whether it will work or not depends a lot on the genome content, how long the stretches of N are and if the regions around it is hard to map to or not, but it might be worth a try?


          Edit: Sorry - I missed the part where it said "single reads".. A bit more tricky then... :/

          Comment

          Latest Articles

          Collapse

          • 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...
            Yesterday, 02:07 PM
          • seqadmin
            Multiomics Techniques Advancing Disease Research
            by seqadmin


            New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

            A major leap in the field has
            ...
            02-08-2024, 06:33 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 02-23-2024, 04:11 PM
          0 responses
          56 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-21-2024, 08:52 AM
          0 responses
          62 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-20-2024, 08:57 AM
          0 responses
          53 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-14-2024, 09:19 AM
          0 responses
          65 views
          0 likes
          Last Post seqadmin  
          Working...
          X