Get ENSEMBL Genomes

A quick and easy way to download all of the CDS, GFF or peptides of predicted genes from the taxa available across the different ENSEMBL Genome portals.

NB Neither this tool nor myself are affiliated witih ENSEMBL, so please use at your own risk and responsibly.

Usage

Decide which genome portal you wish to download from, currently you can choose:

• f for Fungi
• m for Metazoa
• a for Plants (Archaeplastida)
• p for Protists

Then decide which version of the database you wish to download, the current version is 47 as of May 2020.

Peptides (protein/AA) are the default option.

Usage: ./bin/get_ensemble_genomes [-f | -m | -a | -p] -V <int> (-c) (-g)
Databases:
		 -f Ensembl DB: Fungi
		 -m Ensembl DB: Metazoa
		 -a Ensembl DB: Plants
		 -p Ensembl DB: Protists
Version:
		-V Ensembl DB: Version
Other:
 		-c CDS (genes) instead of peptides (default)
 		-g GFF3 instead of FASTA
		-t 'Top Level DNA' aka Chromosomes/Scaffolds - All DNA Regions

For example, to download the CDS for Metazoa:

./bin/get_ensemble_genomes -m -V 47 -c

or to download the gff3 files for Plants:

./bin/get_ensemble_genomes -p -V 47 -g

Other Genome Download Tools

• Get JGI Genomes

Broken?

Sometimes names change or names are slightly different in the table than they are on the ftp, let me know and I'll update to catch the exceptions.