---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2016-03-14 22:52:07+00:00
layout: post
slug: data-received-initial-olympia-oyster-genome-assembly-from-bgi
title: Data Received - Initial Olympia oyster Genome Assembly from BGI
categories:
  - 2016
  - Olympia Oyster Genome Sequencing
tags:
  - assembly
  - BGI
  - olympia oyster
  - Ostrea lurida
  - scaffold
---

The initial assembly of the Ostrea lurida genome is available from BGI. Currently, we've stashed it here:

https://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160314

The data provided consisted of the following three files:




    
  * md5.txt

    
  * N50.txt

    
  * scaffold.fa.fill



md5.txt - Checksum file to verify integrity of files after downloading.

N50.txt - Contains some very limited stats on scaffolds provided.

scaffold.fa.fill - A FASTA file of scaffolds. Since these are scaffolds (and NOT contigs!), there are many regions containing NNNNNN's that have been put in place for scaffold assembly based on paired-end spatial information. As such, the N50 information is not as useful as it would be if these were contigs.

Additional assemblies will be provided at some point. I've emailed BGI about what we should expect from this initial assembly and what subsequent assemblies should look like.