I ran Quast to compare all of our current Olympia oyster genome assemblies.

See Jupyter Notebook in Results section for Quast execution.


Output folder: http://ift.tt/2ig52II

Heatmapped table of results: http://ift.tt/2AFxzya

Very enlightening!


Largest Contig: redundans_sjw_02 (322,397bp)
Total Length: soap_bgi_01 & pbjelly_sjw_01 (697,528,655bp)
Total Length (>=50,000bp): redundans_sjw_03 (17,006,058bp)
N50: redundans_sjw_03 (17,679bp)

Interesting tidbit: The pbjelly_sjw_01 assembly is EXACTLY the same as the soap_bgi_01. Looking at the output messages from that PB Jelly assembly, one can see why. The messages indicate that no gaps were filled on the BGI scaffold reference! That means the PB Jelly output is just the BGI scaffold reference assembly!

Jupyter Notebook (GitHub): 20171114_swoose_oly_assembly_comparisons_quast.ipynb

                    var target_height = $(window).height();

from Sam’s Notebook http://ift.tt/2ii7zly

Assembly Comparison – Oly Assemblies Using Quast
Tagged on: