Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • de novo assembly vs. reference assembly

    Hi,

    I would like to know if someone has experience in comparing a local de novo assembly to a reference assembly and measure which one is the best.

    I have mapped genomic Illumina reads to a reference genome. Then, since I'm interested in a 1Mb region of one of the chromosomes, I used a de novo assembler to assemble the reads that mapped to that 1Mb region. So now I have about 6000 contigs ranging in size from 500bp to 30kb and I would like to:
    1- visualize their position in relation to the original 1Mb region
    2- Be able to say that the de novo local assembly is better (or worse) than just to map my reads to the reference assembly.

    Many thanks

  • #2
    1 E.g. Mauve Contig Mover http://gel.ahabs.wisc.edu/mauve/
    2 What is your definition of 'better' and 'worse'?

    Comment


    • #3
      This is pretty much what Complete Genomics does. They align to the reference and identify positions where they detect a variant, then do local de novo assembly over the variant. It does seem to increase specificity in particular (by excluding potential false positives that disappear after de novo assembly).

      That said, having compared myself, it does not appear to be worth the effort for the relatively long reads you'll get off an Illumina given the computational expense of assembly because it doesn't really seem to increase sensitivity that much.
      Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
      Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
      Projects: U87MG whole genome sequence [Website] [Paper]

      Comment


      • #4
        Thanks for the replies. I would look into the mauve tool.

        By being a 'better' local de novo assembly vs. reference assembly, I consider a region on the genome that has many SNPs, indels, etc. when mapped to a reference assembly. And so, it might be due to a hyper polymorphic region where the reference genome is very different from the sample DNA you are analyzing. In these circumstances I would choose a de novo local assembly.

        Now, the most important question is where do you define a threshold so as you consider a region with "many" variants? That is almost a rhetoric question I guess...

        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
        51 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