---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2017-10-23 19:38:50+00:00
layout: post
slug: assembly-comparison-oly-pacbio-canu-sam-vs-sean-with-quast
title: 'Assembly Comparison - Oly PacBio Canu: Sam vs. Sean with Quast'
categories:
  - 2017
  - Miscellaneous
---

[I recently finished an assembly of our Olympia oyster PacBio data using Canu](https://robertslab.github.io/sams-notebook/posts/2017/2017-10-18-genome-assembly-olympia-oyster-pacbio-canu-v1-6/) and thought it would be interesting to compare to [Sean's Canu assembly](https://genefish.wordpress.com/2017/06/19/seans-notebook-canu-run-finished/).

Granted, this isn't a totally true comparison because I think Sean's assembly is further "polished" using Pilon or something like that, but the Quast analysis is so quick (like < 60 seconds), that it can't hurt.

See the Jupyter Notebook below for the full deets on running Quast.

Results:

Quast output folder: [https://owl.fish.washington.edu/Athaliana/quast_results/results_2017_10_23_18_01_25/](http://owl.fish.washington.edu/Athaliana/quast_results/results_2017_10_23_18_01_25/)

Interactive report: [https://owl.fish.washington.edu/Athaliana/quast_results/results_2017_10_23_18_01_25/report.html](http://owl.fish.washington.edu/Athaliana/quast_results/results_2017_10_23_18_01_25/report.html)

![](https://owl.fish.washington.edu/Athaliana/20171023_quast_sbcanu_sjwcanu.png)(http://owl.fish.washington.edu/Athaliana/20171023_quast_sbcanu_sjwcanu.png)

Jupyter Notebook (GitHub): [20171023_docker_oly_pacbio_canu_comparisons.ipynb](https://github.com/sr320/LabDocs/blob/master/jupyter_nbs/sam/20171023_docker_oly_pacbio_canu_comparisons.ipynb)

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