---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2017-08-28 22:12:42+00:00
layout: post
slug: project-progress-olympia-oyster-genome-assemblies-by-sean-bennett
title: Project Progress - Olympia Oyster Genome Assemblies by Sean Bennett
categories:
  - 2017
  - Olympia Oyster Genome Sequencing
tags:
  - BGI
  - Illumina
  - olympia oyster
  - Ostrea lurida
  - PacBio
---

Here's a brief overview of what [Sean](https://genefish.wordpress.com/author/seanb80/) has done with the Oly genome assembly front.

[Metassembler](https://sourceforge.net/projects/metassembler/)





  * Assemble his BGI assembly and Platanus assembly? Confusing terms here; not sure what he means.


  * Failed due to 32-bit vs. 64-bit installation of MUMmer. He didn't have the chance to re-compile [MUMmer](https://github.com/mummer4/mummer) as 64-bit. However, a [recent MUMmer announcement](http://mummer.sourceforge.net/) suggests that MUMmer can now handle genomes of unlimited size.


  * I believe he was planning on using (or was using?) [GARM](https://garm-meta-assem.sourceforge.net/), which relies upon [MUMmer](https://github.com/mummer4/mummer) and may also include a version of MUMmer (outdated version that led to Sean's error message?).


  * [Notebook entry](https://genefish.wordpress.com/2017/06/27/seans-notebook-mummernucmer-error/)



[Canu](https://github.com/marbl/canu)





  * Assemble [UW PacBio data](https://owl.fish.washington.edu/nightingales/O_lurida/) (filenames beginning with m170211, m170315, m170308, and m170301).


  * Files (including Mox scripts, [Pilon contig polishing](https://github.com/broadinstitute/pilon/wiki), & output FASTA files) are here: [http://owl.fish.washington.edu/scaphapoda/Sean/Oly_Canu_Output/](http://owl.fish.washington.edu/scaphapoda/Sean/Oly_Canu_Output/)


  * [Notebook entry](https://genefish.wordpress.com/2017/06/15/seans-notebook-falcon-out-canu-in/)



[Redundans](https://github.com/lpryszcz/redundans)





  * Assembled [raw Illumina reads provided by BGI](https://owl.fish.washington.edu/nightingales/O_lurida/) (filenames beginning with 15114 and 16103) & [UW PacBio data](http://owl.fish.washington.edu/nightingales/O_lurida/) (filenames beginning with m170211, m170315, m170308, and m170301).


  * Ran this two times.


  * First run



    * Files (does _NOT_ include Mox scripts!) are here: [https://owl.fish.washington.edu/scaphapoda/Sean/Oly_Redundans_Output/](http://owl.fish.washington.edu/scaphapoda/Sean/Oly_Redundans_Output/)


    * [Notebook entry](https://genefish.wordpress.com/2017/05/24/oly-genome-redundans-run-finished/)




  * Second run



    * Files (including Mox scripts & output FASTA files) are here: [https://owl.fish.washington.edu/scaphapoda/Sean/Oly_Redundans_Output_Try_2/](http://owl.fish.washington.edu/scaphapoda/Sean/Oly_Redundans_Output_Try_2/)


    * [Notebook entry](https://genefish.wordpress.com/2017/06/08/seans-notebook-oly-genome-re-assembly-try-2/)





[Platanus](https://platanus.bio.titech.ac.jp/?page_id=14)





  * Assembled [raw Illumina reads provided by BGI](https://owl.fish.washington.edu/nightingales/O_lurida/) (beginning with 151114 and 160103).


  * Ran this two times.


  * First run



    * Files (including Mox scripts & output FASTA files) are here: [https://owl.fish.washington.edu/scaphapoda/Sean/Oly_Illumina_Platanus_Assembly/](http://owl.fish.washington.edu/scaphapoda/Sean/Oly_Illumina_Platanus_Assembly/)


    * [Notebook entry](https://genefish.wordpress.com/2017/05/19/seans-notebook-olympia-oyster-genome/)




  * Second run



    * Files (including Mox scripts & output FASTA files) are here: [https://owl.fish.washington.edu/scaphapoda/Sean/Oly_Platanus_Assembly_Kmer-22/](http://owl.fish.washington.edu/scaphapoda/Sean/Oly_Platanus_Assembly_Kmer-22/)


    * [Notebook entry](https://genefish.wordpress.com/2017/06/02/oly-assembly-try-2-its-yuuuuuuge/)