Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Resolve species/strain in metagenomic bin

    Hi all,

    I am trying to recover microbial draft genomes from metagenomic contigs.

    I have used several assembly and binning tools to optimize my results (CLC, Spades, Vizbin, Maxbin, Metabat).
    Since my samples were dominated by one genus the majority of the contigs belong to this taxa, resulting in one big bin, which based on the number of extracted 16S sequences contains multiple species or even strains of this genus. None of the binning tools I have worked with have been able to resolve the bin, leaving me with one big "pan-genome" bin that is very complete, but also very contaminated (according to checkm).

    What is the best way to resolve the bin? Are other binning softwares that are more accurate? I know of tools that offer metagenomic strain resolution, however usually a database with multiple already sequenced genomes is necessary for those, which in my case is not really the case.

    Thank you for any insights on this topic.

    Daniel

  • #2
    You can give LSA a try. The paper is here http://www.nature.com/nbt/journal/v3.../nbt.3375.html

    Comment


    • #3
      Have you tried MyCC (http://www.nature.com/articles/srep24175)

      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