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This project parses and downloads all the genomic sequences of COVID-19 that were made available by research centres across the world via the website of the National Center for Biotechnology Information (NCBI): Covid-19 page.

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COVID-19 genome Matlab parser

This project parses and downloads all the genomic sequences of COVID-19 that were made available by research centres across the world via the website of the National Center for Biotechnology Information (NCBI): Covid-19 page. In order to reduce stress on the NCBI database, this repo already contains the data up to the time of the latest commit.

Getting Started

These instructions will get you a copy of the project up and running on your machine.

Prerequisites

You need Matlab and the Bioinformatics Toolbox.

I only tested the code on Mac with Matlab2020a. I have no reason to believe it shouldn't run on earlier versions (albeit recent ones), but I won't provide support for any other platform.

Installing

No need for installation. Clone/download and you are ready to go!

Software

In order to avoid repetition of operations that are costly either in terms of computation or bandwidth, the software is divided into steps:

  • step_1_download_genbank - This will download all the sequences into a directory dataset as individual .mat files. Re-running this script will only download files that are not present in the dataset directory, so you can run it again to keep your dataset up-to-date with the NCBI dataset.
  • step_1_download_genbank_yaml_deprecated - This will download all the sequences into a directory dataset as individual .mat files. Re-running this script will only download files that are not present in the dataset directory, so you can run it again to keep your dataset up-to-date with the NCBI dataset. This script uses an old YAML file that NCBI no longer makes available, so running this script will result in a 404 error. The old files associated to this YAML files are still contained in the dataset folder and are bundled together with the new ones.

Structure of dataset

For each entry in the NCBI database, the following information is available:

  • accession - This is the string identifying the specific genome of this entry.
  • collection_date - This is the date of collection, in Matlab's datenum format. To convert to a readable quantity you can run datetime(double(dataset.collection_date),'ConvertFrom','datenum');
  • genebank_entry - This contains the genome bank entry returned by the NCBI database; to access the genomic RNA sequence, you'll refer to dataset.genebank_entry.Sequence.
  • locality - This is the locality of collection (or processing? I am unsure) of the specific genome. When available, not only the country, but also the region/state is specified; in that case, the country and the region/state are separated by a comma.
  • latitude - The approximate latitude corresponding to the locality (this is only available if step 2 was run).
  • longitude - The approximate longitude corresponding to the locality (this is only available if step 2 was run).

Contributing

Pull requests are welcome.

Authors

  • Enzo De Sena - desena.org (enzodesena AT gmail DOT com)

The project uses:

License

This project is licensed under the MIT License. The data and the sofware are provided as they are without warranty of any kind (see LICENSE.md for details).

About

This project parses and downloads all the genomic sequences of COVID-19 that were made available by research centres across the world via the website of the National Center for Biotechnology Information (NCBI): Covid-19 page.

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