Assembly Comparisons – Oly Assemblies Using Quast

2018
Olympia Oyster Genome Sequencing
assembly
jupyter notebook
Olympia oyster
Ostrea lurida
QUAST
Author

Sam White

Published

January 16, 2018

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

See Jupyter Notebook in Results section for Quast execution.

Results:

Output folder: https://owl.fish.washington.edu/Athaliana/quast_results/results_2018_01_16_10_08_35/

Heatmapped table of results: https://owl.fish.washington.edu/Athaliana/quast_results/results_2018_01_16_10_08_35/report.html

Very enlightening!

After all the difficulties with PB Jelly, it has produced the most large contigs. However, it does also have the highest quantity and rate of N’s of all the assemblies produced to date.

BEST OF:

contigs (>= 50000 bp): pbjelly_sjw_01 (894)

Largest Contig: redundans_sjw_02 (322,397bp) Total Length: pbjelly_sjw_01 (1,180,563,613bp) Total Length (>=50,000bp): pbjelly_sjw_01 (57,741,906bp) N50: redundans_sjw_03 (17,679bp)

Jupyter Notebook (GitHub): 20180116_swoose_oly_assembly_comparisons_quast.ipynb