ncbiDownload

This script takes a species_list.txt and downloads all the genomes and (proteomes, gtf, and feature tables) if available, of the species in the list.

Notes

• Make sure NCBI has the genome of the species.
• If the genome is not annotated, set the annotated variable to false in the script..
• make sure the last line of the species_list.txt is an empty new line and not a species' name.

Quick Start

Clone this repository:

git clone https://github.com/lazobax/ncbiDownload.git

Move to directory and create conda environment, activate the environment:

cd ncbiDownload
conda env create -f environment.yaml
conda activate ncbi-datasets

Run the script after configuration:

bash download.sh

Raise issues if found.