Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • hybrid assembly for PacBio and Illumina data

    I am working on a project in which we have sequence data on the same regions and individuals from Pacific Biosciences and Illumina. The PacBio reads are much longer (around 2400 bp) but the Illumina reads (only 100 bp long) are of higher quality. We are interested in doing de novo assembly with the PacBio reads to build a scaffold and then would like to map the Illumina reads to it.

    There was a prior post on this but it is from mid-2009. http://seqanswers.com/forums/showthread.php?t=10401

    What are the current methods to do this kind of hybrid assembly? What methods have been found to work particularly well?

  • #2
    The new v1.3 release from PacBio supposedly supports hybrid assembly, I have not made much attempt to get it to work since we had already implemented a pipeline based on the PacBioToCA plug-in for the Celera Assembler that was written by Sergey Koren at NBACC. This script uses short read, high quality data to error correct the PacBio reads and outputs a .frg file suitable for OLC assembly in CA. We have been able to create single-contig chromosomes of bacteria with no finishing steps using this approach, for several different species. Some species with very large repetitive phage integrations are more difficult if you need to know exactly which slight variants of these are in which chromosomal position.

    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
    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
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X