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
- GNU Bash.
- curl.
§ 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'.