---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2016-05-16 20:31:04+00:00
layout: post
slug: data-management-olympia-oyster-small-insert-library-genome-assembly-from-bgi
title: Data Management - Olympia Oyster Small Insert Library Genome Assembly from
  BGI
categories:
  - 2016
  - Olympia Oyster Genome Sequencing
tags:
  - BGI
  - ipython notebook
  - jupyter notebook
  - olympia oyster
  - Ostrea lurida
---

Received another set of _Ostrea lurida_ genome assembly data from BGI. In this case, it's data assembled from the small insert libraries they created for this project.

All data is stored here: [https://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160512/](http://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160512/)

They've provided a [Genome Survey (PDF)(https://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160512/20160512_F15FTSUSAT0327_genome_survey.pdf) that has some info about the data they've assembled. In it, is the estimated genome size:

Olympia oyster genome size: 1898.92 Mb

Additionally, there's a table breaking down the N50 distributions of scaffold and contig sizes.

Data management stuff was performed in a Jupyter (iPython) notebook; see below.

Jupyter Notebook: [20160516_Oly_Small_Insert_Library_Genome_Read_Counts.ipynb](https://github.com/sr320/LabDocs/blob/master/jupyter_nbs/sam/20160516_Oly_Small_Insert_Library_Genome_Read_Counts.ipynb)

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