Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Assembly of a mycete genome with HGAP4

    Hello,

    I need to assemble a fungus genome for which no information is known. When doing the assembly with canu, I get an assembly of 4918 contigs with a total of 57 123 496 bp. However, with HGAP4, I get an assembly of 2617 contigs with a total of 27,258,314 bp. Why such a big difference? Is it because the genome is diploid and HGAP4 assembles only one haplotype while canu assembles both?

    Thank you,

    Antony
    Last edited by Antony03; 04-10-2018, 12:02 PM.

  • #2
    It's possible that ploidy could account for some of the difference, but it is unlikely that it is that simple. Using default parameters I wouldn't expect Canu to not collapse haplotypes and Falcon to fully collapse, although with the correct parameters and enough divergence between haplotypes both assemblers theoretically could.
    Some things to try:
    1. Align assemblies to one another to see what the difference actually is, for a quick visulization, http://assemblytics.com/
    2. Look at the alternate contigs in the HGAP.4 assembly, <HGAP.4 job dir>/tasks/falcon_ns.tasks.task_falcon2_run_asm-0/a_ctg.fa. HGAP.4 is based on Falcon so does generate contigs for possible alternate haplotypes http://pb-falcon.readthedocs.io/en/latest/
    Some more resources on diploid assembly: http://pb-falcon.readthedocs.io/en/l...PacBioHops.pdf
    http://pb-falcon.readthedocs.io/en/l...idsPAG2018.pdf

    Comment


    • #3
      Originally posted by Antony03 View Post
      Hello,

      I need to assemble a fungus genome for which no information is known. When doing the assembly with canu, I get an assembly of 4918 contigs with a total of 57 123 496 bp. However, with HGAP4, I get an assembly of 2617 contigs with a total of 27,258,314 bp. Why such a big difference? Is it because the genome is diploid and HGAP4 assembles only one haplotype while canu assembles both?

      Thank you,

      Antony
      Curious as to how long the HGAP4 assembler took and what were the specs on your computer/cluster?

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Best Practices for Single-Cell Sequencing Analysis
        by seqadmin



        While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
        06-06-2024, 07:15 AM
      • seqadmin
        Latest Developments in Precision Medicine
        by seqadmin



        Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

        Somatic Genomics
        “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
        05-24-2024, 01:16 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 08:58 AM
      0 responses
      9 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-12-2024, 02:20 PM
      0 responses
      15 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-07-2024, 06:58 AM
      0 responses
      182 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-06-2024, 08:18 AM
      0 responses
      231 views
      0 likes
      Last Post seqadmin  
      Working...
      X