Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Scaffolding a highly repetitive genome

    Hi all,

    I'm working through a difficult region in a highly repetitive plant genome. I've got 30 BACs sequenced and assembled into contigs for this region, but the physical map is still incomplete. Using whole genome paired end and mate pair Illumina libraries from 130nt up to 40kb inserts, I'm trying to scaffold these BACs together, but the high transposon content is causing me to have trust issues.

    I've used SSPACE to scaffold these before, but when nearly 80% of some BACs is repetitive, I don't trust it. I'm going to use SSPACE again on a repeatmasked version of the BACs, but aside from that, does anyone have suggestions on scaffolding highly repetitive BACs?

    Thanks!
    Alex
    Last edited by aharkess; 12-08-2012, 11:01 AM.
    ==========
    Alex Harkess
    Leebens-Mack Lab
    Plant Biology Department
    University of Georgia, Athens GA

  • #2
    What TEs make up the repetitive elements? If you have a library of well-annotated LTRs or some DNA transposons you could use the TSD + terminal sequences to scaffold contigs together. Its painstaking work, but its been shown to work in a few complex genomes like barley and wheat

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Quality Control Essentials for Next-Generation Sequencing Workflows
      by seqadmin




      Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

      Nucleic Acid Quality Control
      Preparing for NGS starts with isolating the...
      02-10-2025, 01:58 PM
    • seqadmin
      An Introduction to the Technologies Transforming Precision Medicine
      by seqadmin


      In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...
      01-27-2025, 07:46 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 02-07-2025, 09:30 AM
    0 responses
    54 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-05-2025, 10:34 AM
    0 responses
    88 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-03-2025, 09:07 AM
    0 responses
    70 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 01-31-2025, 08:31 AM
    0 responses
    44 views
    0 likes
    Last Post seqadmin  
    Working...
    X