NCBI Genome Downloading Scripts

Some script to download bacterial and fungal genomes from NCBI after they restructured their FTP a while ago.

Idea shamelessly stolen from Mick Watson's Kraken downloader scripts that can also be found in Mick's GitHub repo. However, Mick's scripts are ~~written in Perl~~ specific to actually building a Kraken database (as advertised).

So this is a set of scripts that focuses on the actual genome downloading.

Installation

pip install ncbi-genome-download

Alternatively, clone this repository from GitHub, then run (in a python virtual environment)

pip install .

To download all bacterial RefSeq genomes in GenBank format from NCBI, run the following:

ncbi-genome-download bacteria

To download all fungal GenBank genomes from NCBI in GenBank format, run:

ncbi-genome-download --section genbank fungi

To download all viral RefSeq genomes in FASTA format, run:

ncbi-genome-download --format fasta viral

To get an overview of all options, run

ncbi-genome-download --help

All code is available under the Apache License version 2, see the LICENSE file for details.