Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • diego diaz
    Member
    • Oct 2013
    • 62

    Basic question about concept of contig

    Hi,

    I have a little doubt about the definition of a contig. According to Google, It is a set of overlapping DNA segments that together represent a consensus region of DNA. This description makes sense when we are performing denovo assemblies, but when we are mapping reads to a reference genome, is It correct to call contigs certain regions where several reads were mapped?

    Thanks in advance!
  • Brian Bushnell
    Super Moderator
    • Jan 2014
    • 2709

    #2
    A contig is a contiguous sequence of defined DNA. The definition you found is incorrect.

    When you map, the contigs are already defined in the reference regardless of mapping results. Within the reference, a sequence of letters ACGT bounded on either end by Ns represents a contig.

    Comment

    • diego diaz
      Member
      • Oct 2013
      • 62

      #3
      Originally posted by Brian Bushnell View Post
      A contig is a contiguous sequence of defined DNA. The definition you found is incorrect.

      When you map, the contigs are already defined in the reference regardless of mapping results. Within the reference, a sequence of letters ACGT bounded on either end by Ns represents a contig.
      Thanks

      This afternoon I had a little discussion about definition of contigs with a person in my lab. He argued that, for example, when we map a set of miRNAs reads to a reference genome, we can extract the regions where the reads were mapped and call these regions contigs, because a set of "contiguous" reads were mapped there. I think this is a wrong concept of contig right?

      My concept of contig is similar to that you mentioned.

      Comment

      • Brian Bushnell
        Super Moderator
        • Jan 2014
        • 2709

        #4
        That's correct; contigs are not defined by mapping, they are inherent to the reference.

        Comment

        • diego diaz
          Member
          • Oct 2013
          • 62

          #5
          Thanks again

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Pathogen Surveillance with Advanced Genomic Tools
            by seqadmin




            The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
            03-24-2025, 11:48 AM
          • seqadmin
            New Genomics Tools and Methods Shared at AGBT 2025
            by seqadmin


            This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

            The Headliner
            The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
            03-03-2025, 01:39 PM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 03-20-2025, 05:03 AM
          0 responses
          49 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, 03-19-2025, 07:27 AM
          0 responses
          57 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, 03-18-2025, 12:50 PM
          0 responses
          50 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, 03-03-2025, 01:15 PM
          0 responses
          201 views
          0 reactions
          Last Post seqadmin  
          Working...