GenomeDatabase

Genome Database - A tool to create a local database of reference genome sequences

Usage: java path/to/GenomeDatabase.jar [options]

By Marc Strous, 2016

This tool enables you to download fasta files of protein and RNA sequences encoded
in reference genomes at NCBI. You can select relevant genomes with a set of queries.
Each query has four fields, separated by comma's. Example of a queries are:

superkingdom,Bacteria,genus,ftp
superkingdom,Archaea,genus,ftp
superkingdom,Eukaryota,phylum,ftp
superkingdom,Viruses,family,elink

The first query would download (with ftp) all available reference genomes of the
superkingdom Bacteria, limited to one genome per genus. The second query would do
the same for superkingdom Archaea. The third would download all Eukaryotic genomes,
a single representative for each phylum. The fourth would download all available
viral genomes, one representative per family, using the ncbi elink tool.