Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Why is predicted best k for de novo assembly so different from actual best k?

    Greetings everyone,

    I’m doing my first genome assembly for a non-model plant species, and I need some insight about best kmer lengths for DBG-based assembly. My NGS data is a full lane of Illumina HiSeq V4 2x125 with a single library of insert size 350. Using kmer-counting methods, such as Jellyfish, my predicted best value k has ranged from 93-101 due to the large number of reads and their relatively-long length for HiSeq reads.

    However, I have found all of my highest-quality assemblies at kmer-lengths <40, with my highest N50 and CEGs-mapped occurring at lengths 29 and 33, respectively. Does anyone know why I’m seeing such a large difference between predicted best k and actual best k? Given that it’s a discrepancy of more than 50bp, I feel like there’s got to be a common explanation that googling simply hasn’t turned up. I predict it’s related to heterogeneity in the reads, but I’m unable to find much elaboration on the effect of heterogeneous reads, so thanks for any insights!

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...
    05-06-2024, 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, 05-14-2024, 07:03 AM
0 responses
25 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-10-2024, 06:35 AM
0 responses
45 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-09-2024, 02:46 PM
0 responses
59 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-07-2024, 06:57 AM
0 responses
46 views
0 likes
Last Post seqadmin  
Working...
X