---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2016-12-15 22:46:19+00:00
layout: post
slug: data-management-integrity-check-of-final-bgi-olympia-oyster-geoduck-data
title: Data Management - Integrity Check of Final BGI Olympia Oyster & Geoduck Data
categories:
  - 2016
  - Geoduck Genome Sequencing
  - Olympia Oyster Genome Sequencing
tags:
  - array
  - bash
  - BGI
  - checksum
  - geoduck
  - jupyter notebook
  - md5
  - olympia oyster
  - Ostrea lurida
  - ostrich
  - Panopea generosa
  - parameter substitution
---

After completing the downloads of these files from BGI, I needed to verify that the downloaded copies matched the originals. Below is a Jupyter Notebook detailing how I verified file integrity via MD5 checksums. It also highlights the importance of doing this check when working with large sequencing files (or, just large files in general), as a few of them had mis-matching MD5 checksums!

Although the notebook is embedded below, it might be easier viewing via the notebook link (hosted on GitHub).

At the end of the day, I had to re-download some files, but all the MD5 checksums match and these data are ready for analysis:

[Final _Ostrea lurida_ genome files](https://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/)

[Final _Panopea generosa_ genome files](https://owl.fish.washington.edu/P_generosa_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Panopea_generosa/)

Jupyter Notebook: [20161214_docker_BGI_data_integrity_check.ipynb](https://github.com/sr320/LabDocs/blob/master/jupyter_nbs/sam/20161214_docker_BGI_data_integrity_check.ipynb)

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