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.

Results:

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:http://ift.tt/2yuNMsP

QUAST comparison using –scaffolds setting:

Interactive link: http://ift.tt/2yuNMZR

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from Sam’s Notebook http://ift.tt/2xomQ9r

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