How to download genomes and proteins from JGI in bulk via the command line?
I'm trying to figure out how to download from JGI in bulk. In particular, I'd like to grab the genome and MycoCosm (https://mycocosm.jgi.doe.gov/). I honestly have no idea where to start. I see that there is something called Globus but I'm not familiar with this service and the tutorials I've found seem to be dated. With NCBI, I can use ncbi-genome-download with a command like this:
ncbi-genome-download --section genbank --formats fasta,gff,protein-fasta,cds-fasta,assembly-stats --assembly-levels all --parallel 64 --progress-bar fungi
Is there any tool that can do this or something similar with JGI genomes?
In particular, with publicly available genomes.
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You probably know about https://github.com/glarue/jgi-query already?
It is not going to be as simple to download from JGI compared to NCBI.