Enveomics collection

A toolbox for microbial genomics and metagenomics

RefSeq.download.bash

Downloads a collection of sequences and/or annotations from NCBI's RefSeq.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

§ Usage

RefSeq.download.bash string string string [opts]

§ Arguments

Organism*
 string  The organism to download (e.g., Streptococcus_pneumoniae).
Extension*
 string  Extension to download. Common extensions include .fna.gz (genomic sequences), .faa.gz (protein sequences), .gff.gz (annotations), and .*.gz (all data).
Level*
 string  Use only genomes with this assembly level. Common levels are 'Complete Genome' and 'Contig'. By default, any assembly level is allowed ('Any').
Directory
 out_dir  Directory where the files are to be downladed. By default, same as 'Organism'.
* Mandatory.