---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2018-08-23 15:47:04+00:00
layout: post
slug: assembly-stats-geoduck-hi-c-final-assembly-comparison
title: Assembly Stats – Geoduck Hi-C Final Assembly Comparison
categories:
  - 2018
  - Geoduck Genome Sequencing
tags:
  - assembly
  - genome
  - geoduck
  - Panopea generosa
  - phase genomics
  - QUAST
---

We received the final geoduck genome assembly data from Phase Genomics, in which they updated the assembly by performing some manual curation:





  * [geoduck_manual_scaffolds.fasta](https://owl.fish.washington.edu/Athaliana/20180822_phase_genomics_geoduck_Results/geoduck_manual/geoduck_manual_scaffolds.fasta)



There are additional assembly files that provide some additional assembly data. See the following directory:



  * [20180822_phase_genomics_geoduck_Results/geoduck_manual/](https://owl.fish.washington.edu/Athaliana/20180822_phase_genomics_geoduck_Results/geoduck_manual/)



Actual sequencing data and two previous assemblies were [previously received on 20180421](https://robertslab.github.io/sams-notebook/posts/2018/2018-04-21-data-management-geoduck-phase-genomics-hi-c-data/).

All assembly data (both old and new) from Phase Genomics was downloaded in full from the Google Drive link provided by them and stored here on Owl:





  * [20180822_phase_genomics_geoduck_Results/](https://owl.fish.washington.edu/Athaliana/20180822_phase_genomics_geoduck_Results/)



Ran Quast to compare all three assemblies provided (command run on Swoose):


    
    <code>
    /home/sam/software/quast-4.5/quast.py \
    -t 24 \
    --labels 20180403_pga,20180421_pga,20180810_geo_manual \
    /mnt/owl/Athaliana/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-03 11:05:41.596285/PGA_assembly.fasta \ /mnt/owl/Athaliana/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/PGA_assembly.fasta \ /mnt/owl/Athaliana/20180822_phase_genomics_geoduck_Results/geoduck_manual/geoduck_manual_scaffolds.fasta
    </code>





* * *





#### Results:



Quast output folder: [results_2018_08_23_07_38_28/](https://owl.fish.washington.edu/Athaliana/quast_results/results_2018_08_23_07_38_28/)

Quast report (HTML): [results_2018_08_23_07_38_28/report.html](https://owl.fish.washington.edu/Athaliana/quast_results/results_2018_08_23_07_38_28/report.html)

![](https://owl.fish.washington.edu/Athaliana/quast_results/results_2018_08_23_07_38_28/20180823_quast_geoduck_pga.png)
