Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • SPAdes: does contig with node id has/refer coverage?

    Hi Members,
    I'm working on bacteria genome, illumina Hiseq paired end reads.
    Used:
    - trimmomatic with illumina adapter file.
    - spades for assembly with careful flag, bayes hammer correction.

    I get 2 fasta files: contigs and scaffolds.
    Contigs and scaffolds file give output in below fashion:

    scaffolds-
    >NODE_452_length_82_cov_291.815_ID_903
    contigs-
    >NODE_488_length_109_cov_1.07407_ID_975
    My question:
    Does cov_1.07407 and cov_291.815 refer to coverage of the contig/scaffold?

    Thank you.
    Bioinformaticscally calm

  • #2
    Yes, like in Velvet, this is the average k-mer coverage of a contig/scaffold. Use the last k-mer length if you need to convert to read coverage.

    Comment


    • #3
      Hi,
      Thanks for your reply.
      I do not quite understand what you meant. I have not really well read/understood on Velvet. (Have basic knowledge that it works on de bruijn graphs and so so..)

      Originally posted by akorobeynikov View Post
      Yes, like in Velvet, this is the average k-mer coverage of a contig/scaffold. Use the last k-mer length if you need to convert to read coverage.
      My assembly ran on 21, 33 and 55 k-mer (default SPAdes run).
      Bioinformaticscally calm

      Comment


      • #4
        Originally posted by bio_informatics View Post
        Hi,
        Thanks for your reply.
        I do not quite understand what you meant. I have not really well read/understood on Velvet. (Have basic knowledge that it works on de bruijn graphs and so so..)



        My assembly ran on 21, 33 and 55 k-mer (default SPAdes run).
        Check this http://seqanswers.com/forums/showthread.php?t=1529 for k-mer coverage. Use k=55 for SPAdes in this case.

        Comment


        • #5
          Thank you for directing to that page.

          Indeed the below URL far better explains what I was looking for:

          Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


          Merci!
          Bioinformaticscally calm

          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
          10 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 06:07 PM
          0 responses
          9 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          50 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