{"repo":"kblin/ncbi-genome-download","free":true,"listed":false,"github":"https://github.com/kblin/ncbi-genome-download","clone":"git clone https://github.com/kblin/ncbi-genome-download.git","description":"Scripts to download genomes from the NCBI FTP servers","language":"Python","stars":1083,"topics":["ncbi","bioinformatics","download-genomes","python","biology","genomics","command-line","genbank"],"license":"Apache-2.0","category":"cli-tools","readme_excerpt":"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 Alternatively, clone this repository from GitHub, then run (in a python virtual environment) If this fails on older versions of Python, try updating your pip tool first: and then rerun the ncbi-genome-download install. Alternatively, ncbi-genome-download is packaged in conda . Refer the the Anaconda/miniconda site to install a distribution (highly recommended). With that installed one can do: 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 3.9, 3.10, 3.11, 3.12, and 3.13. Specifically, no attempt at testing under Python versions older than 3.9 is being made. If your system is stuck on an older version of Python, consider using a tool like Homebrew to obtain a more up-to-date version. ncbi-genome-download 0.2.12 was the last version to support Python 2. Usage To download all bacterial RefSeq genomes in GenBank format from NCBI, run the following: Downloading multiple groups is also possible: Note : To see all available groups, ","default_branch":null,"files":null,"tree":[],"storefront":"/r/kblin","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/kblin/ncbi-genome-download/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}