ncbi-genome-download 0.1.8

Download genome files from the NCBI FTP server.

# NCBI Genome Downloading Scripts

[](http://github.drone.secondarymetabolites.org/kblin/ncbi-genome-download) [](https://landscape.io/github/kblin/ncbi-genome-download/master)

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 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 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.