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 .

ncbi-genome-download is only developed and tested on Python releases still under active support by the Python project. At the moment, this means versions 2.7, 3.3, 3.4, 3.5 and 3.6. Specifically, no attempt at testing under Python versions older than 2.7 or 3.3 is being made.

If your system is stuck on an older version of Python, consider using a tool like Homebrew or Linuxbrew to obtain a more up-to-date version.

Usage

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

ncbi-genome-download bacteria

If you're on a reasonably fast connection, you might want to try running multiple downloads in parallel:

ncbi-genome-download bacteria --parallel 4

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 download only completed bacterial RefSeq genomes in GenBank format, run:

ncbi-genome-download --assembly-level complete bacteria

To download bacterial RefSeq genomes of the genus Streptomyces, run:

ncbi-genome-download --genus Streptomyces bacteria

Note: This is a simple string match on the organism name provided by NCBI only.

To download bacterial RefSeq genomes based on their NCBI species taxonomy ID, run:

ncbi-genome-download --species-taxid 562 bacteria

Note: The above command will download all RefSeq genomes belonging to Escherichia coli.

To download a specific bacterial RefSeq genomes based on its NCBI taxonomy ID, run:

ncbi-genome-download --taxid 511145 bacteria

Note: The above command will download the RefSeq genome belonging to Escherichia coli str. K-12 substr. MG1655.

To get an overview of all options, run

ncbi-genome-download --help

License

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