Provided by: centrifuge_1.0.3-1_amd64
centrifuge-download - centrifuge helper to download databases
centrifuge-download [<options>] <database> ARGUMENT <database> One of refseq, genbank, contaminants or taxonomy: - use refseq or genbank for genomic sequences, - contaminants gets contaminant sequences from UniVec and EmVec, - taxonomy for taxonomy mappings. COMMON OPTIONS -o <directory> Folder to which the files are downloaded. Default: '.'. -P <# of threads> Number of processes when downloading (uses xargs). Default: '1' WHEN USING database refseq OR genbank: -d <domain> What domain to download. One or more of bacteria, viral, archaea, fungi, protozoa, invertebrate, plant, vertebrate_mammalian, vertebrate_other (comma separated). -a <assembly level> Only download genomes with the specified assembly level. Default: 'Complete Genome'. -c <refseq category> Only download genomes in the specified refseq category. Default: any. -t <taxids> Only download the specified taxonomy IDs, comma separated. Default: any. -r Download RNA sequences, too. -u Filter unplaced sequences. -m Mask low-complexity regions using dustmasker. Default: off. -l Modify header to include taxonomy ID. Default: off. -g Download GI map.
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.