Genome Assembly - Olympia oyster Redundans/Canu vs. Redundans/Racon

Decided to compare the Redundans using Canu as reference and Redundans using Racon as reference. Both reference assemblies were just our PacBio data.

Jupyter notebook (GitHub): 20171005_docker_oly_redundans.ipynb

Notebook is also embedded at the end of this post.


It should be noted that the paired reads for each of the BGI mate-pair Illumina data did not assemble, just like last time I used them:

  • 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.gz

  • 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.gz

  • 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.gz

  • 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.gz

  • 160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz

  • 160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.gz

Redundans with Canu is better, suggesting that the Canu assembly is the better of the two PacBio assemblies (which we had already suspected).

QUAST comparison using default settings:

Interactive link:


QUAST comparison using –scaffolds setting:

Interactive link: