Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bbtools/BBmaps output questions

    Hello, I am using "stats.sh" command in BBtools to check my assembled metagenomes. I am looking for N50 and the largest contig. In my case, there is a line shows "Main genome contig N/L50: 7688/759" and "Max contig length: 5.905 KB". I know N50 and L50? What is N/L50 here? Does this mean N50 = 7688 and L50=759? Why my max contig length is shorter than N50? Is this possbile? (details see attached files)

    A C G T N IUPAC Other GC GC_stdev
    0.2126 0.2873 0.2874 0.2127 0.0000 0.0000 0.0000 0.5747 0.0976

    Main genome scaffold total: 19074
    Main genome contig total: 19074
    Main genome scaffold sequence total: 15.193 MB
    Main genome contig sequence total: 15.193 MB 0.000% gap
    Main genome scaffold N/L50: 7688/759
    Main genome contig N/L50: 7688/759
    Main genome scaffold N/L90: 16532/636
    Main genome contig N/L90: 16532/636
    Max scaffold length: 5.905 KB
    Max contig length: 5.905 KB
    Number of scaffolds > 50 KB: 0
    % main genome in scaffolds > 50 KB: 0.00%
    Attached Files

  • #2
    Originally posted by SDPA_Pet View Post
    Does this mean N50 = 7688 and L50=759?
    Yes, that is what that means.
    Why my max contig length is shorter than N50? Is this possbile?
    Because Brian believes (and I agree with him, not that he requires any validation from me) the proper notation should be N50=number of contigs making 50% of your assembly and L50=length lower limit of contigs making up 50% of your assembly. So what stats.sh is telling you is that the largest 7,688 contigs account for 50% of your assembly length and those contigs are all ≥ 759bp.

    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, 03-27-2024, 06:37 PM
    0 responses
    12 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-27-2024, 06:07 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    53 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    69 views
    0 likes
    Last Post seqadmin  
    Working...
    X