Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Which coverage for resequencing genome

    hey, I would like to sequence a genome (~800 MB). We have already the genome of the same species but different strain sequenced with 90x. Which coverage is recommended for resequencing genomes on a hiseq? I would like to identify snps, structural variations, genome rearangements (....) afterwards.
    thanks
    Alex

  • #2
    I suppose that means you have a reference sequence. Then I think 30x is enough if you use PCR-free kit. But most likely you don't have 1-2ug DNA, then 60x is more appropriate. If your genome is AT-rich, you might want to need to do some special treatment.

    Comment


    • #3
      I have another question regarding the resequencing project. What methods are commonly applied to subsequenctly assemble the genome when a related reference genome is available. I found velvet (columbus variante) and samtools also provide also a function for assembling mapped reads (mpileup). Is there a standard program for assembling genomes using reference based approaches?
      Many thanks in advance.
      Alex

      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
      12 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