Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Detecting Known, Low Frequency SNPs in evolving bacterial communities

    Hi all,

    I'm using NGS data to observe how a community of congenic bacteria evolve over time. Basically, I'm starting by inputting several different alleles of one gene into the same medium and seeing how that population changes over time by sequencing the DNA of that gene.

    As far as I can tell, all the SNP calling pipelines appear to be more for genome wide discovery than something like what I am doing.

    Currently, I am using VarScan and LoFreq to determine the allele frequencies in this community. The agreement between the two pipelines is decent, but as of now VarScan doesn't seem to be able to detect samples that are present in less than 20% of the population (despite what was reported in this paper and all the other programs are reported to be even worse) and I would like to be able to use at least two different programs to verify the presence of these alleles.

    Does anyone know of a better low frequency SNP calling pipeline or perhaps a program that allows you to call SNPs based on known alleles (this would actually be the ideal, but I haven't seen anything like this anywhere that I've read)?

    Thanks!

    P.S. I'm relatively new to NGS work so please bear with me if I've made some egregious oversight here.

  • #2
    I have been really pleased with using the variant caller that is a part of the BBTools package for rare variants in mitochondrial DNA.

    It is not so well documented at that site, but look here for how to use:
    Multi-threaded Distributed Memory Overlap-Layout-Consensus (OLC) Metagenome Assembler - abiswas-odu/Disco

    or throughout this forum.

    Comment


    • #3
      Thank you very much for your recommendation, I'll be sure to check it out!

      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
      49 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