ncbi-genome-download 0.1.1

Download genome files from the NCBI FTP server.

# 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](http://www.opiniomics.org/building-a-kraken-database-with-new-ftp-structure-and-no-gi-numbers/) that can also be found in [Mick’s GitHub repo](https://github.com/mw55309/Kraken_db_install_scripts). 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 . `

## Usage

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

` ncbi-genome-download bacteria `

To download all fungal GenBank genomes from NCBI, run: ` ncbi-genome-download --section genbank fungi `

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](LICENSE) file for details.