Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • de novo assembly (velvet or others)

    Dear all,

    is velvet (or others) able to use a read twice in the assembly of two different contigs or does velvet need in this case two duplicates of this read?

    It could be that in certain genes highly conserved domains are present. In order to be able to assemble the different genes, certain reads could be used more than once. Is this possible in velvet (or others)?

    The reason why I ask this is because I filter my dataset for duplicated reads, thereby only keeping the "unique" ones. But I wonder now if I do not lose information by doing this. If velvet (or others) is able to use reads more than once, the filtering is fine; if not, I should keep all my reads.

    Any comments more than welcome.

    Many thanks in advance,

    Steven

  • #2
    Velvet and other de Bruijn graph assemblers (abyss, Euler-SR) are able to re-use reads. Each instance of the read contributes the same k-mer path to the graph so removing redundant copies does not effect the structure of the graph. That said, you should not filter the data as most assemblers track the number of times each k-mer exists in the input data. This information is used for error correction/removal and to infer the copy count for each segment in the graph which can help resolve repeats.

    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