Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • After genome assembly...

    ...what to do?
    Hi, I've been working a little with a large genome assembly (250Mb). I have Illumina and PacBio reads using diffrent approaches. At the end, used SPAdes assembly with Illumina data and PBJelly for filling gaps with PacBio subreads. Decent assembly at the end.
    But when I compare the assembly with some regions I have already sequenced, looks like the assembly can still be improved. Situations like this are found:

    Code:
    reference: ****************************************************************************************
    contigs:    -------------------------------                              -----------------------------------
                                          -----------------------------------------------
    where there are overlapping regions of 70-75 nt with 100% identity.
    Is there any post assembly processor which would be able to deal with situations like this?
    Thanks

  • #2
    70bp overlap with 100% identity should not be joined, in general. That's too short and would cause rampant misassemblies if you instituted it as a general policy. Besides, do you know that the reference in this case is actually correct?

    I could be wrong, but I thought that recent versions of PBJelly did try to join contigs that had sufficient support.

    I wrote a program called Dedupe that will find all of these overlaps:

    dedupe.sh in=contigs.fa am=t ac=f fo=t mo=70 ngn=f dot=graph.dot

    This will find and print all the overlaps of at least 70bp with 100% identity (annotated by the overlap length, coordinates, and number of substitutions/edits). You can allow a fixed number of edits or substitutions in the overlap region with the "e=" or "s=" flag.

    It won't merge anything, though it would be nice if someone wrote a post-processing program that used the overlap information to do merging. Still, 70bp is too short.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Recent Advances in Sequencing Analysis Tools
      by seqadmin


      The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
      Today, 07:48 AM
    • seqadmin
      Essential Discoveries and Tools in Epitranscriptomics
      by seqadmin




      The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
      04-22-2024, 07:01 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Today, 07:17 AM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-02-2024, 08:06 AM
    0 responses
    19 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-30-2024, 12:17 PM
    0 responses
    20 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-29-2024, 10:49 AM
    0 responses
    28 views
    0 likes
    Last Post seqadmin  
    Working...
    X