Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • #16
    Well... if there is a reference, I would compare them to the reference. With or without a reference, I think Quast is fairly useful. It tells you the number of predicted genes and so forth in your assembly; generally, the more longer genes you have and the fewer shorter genes, the higher the assembly quality. Most useful if you have more than one assembly. If you have a reference, it will also tell you the number of misassemblies.

    Similarly, if you map all of the source reads to the assembly, then the number of non-match symbols (insertions, deletions, substitutions) correlates with assembly quality, as does % of reads mapped, % paired, and % unambiguous mappings. We use BBMap for that purpose here, though again, it's better for determining the relative quality of two assemblies than the absolute quality of one assembly. You can also try ALE, which attempts to judge the probability of an assembly being correct given the reads. This is based on mismatches, deviation of paired insert size from normal, and coverage depth.

    If you have EST data, then calculating the EST capture rate is also very useful in determining genome completeness and misassemblies.

    Incidentally, I think Q30 is much too high for trimming. Also, what trimming tool are you using? In my tests, the top performing ones use the phred algorithm (this includes seqtk and my own); all other algorithms were consistently inferior. The attached graph shows error rate of reads versus bases remaining from the initial 150Mbp dataset after quality-trimming; each point represents a different quality cutoff (so the leftmost point is trimming to Q40, then Q39, etc). The black line is the best, but that uses error-correction AND quality-trimming; all the others just use quality-trimming. seqtk and bbtrim appear to be identical. The error rates were calculated by mapping back to the Pedobacter reference.
    Attached Files
    Last edited by Brian Bushnell; 02-21-2014, 05:28 PM.

    Comment


    • #17
      Yes, there is a reference that is pretty close, <2% difference at the base level, with a few rearrangements likely. I use Btrim for the trimming.

      Comment


      • #18
        Originally posted by Genomics101 View Post
        Yes, there is a reference that is pretty close, <2% difference at the base level, with a few rearrangements likely. I use Btrim for the trimming.
        Sounds close enough to use Quast to get a very good idea of assembly quality. You can run it with the assembly and reference as the inputs and it will tell you the quality of the assembly with respect to the reference. Even with 2% difference and some rearrangements, the assembly closest to the reference should be the highest quality assembly.

        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
        11 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        51 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        68 views
        0 likes
        Last Post seqadmin  
        Working...
        X