DOKK / manpages / debian 11 / centrifuge / centrifuge-download.1.en

centrifuge-download - centrifuge helper to download databases

centrifuge-download [<options>] <database>


One of refseq, genbank, contaminants or taxonomy:
- contaminants gets contaminant sequences from UniVec and EmVec, - taxonomy for taxonomy mappings.


Folder to which the files are downloaded. Default: '.'.
Number of processes when downloading (uses xargs). Default: '1'

What domain to download. One or more of bacteria, viral, archaea, fungi, protozoa, invertebrate, plant, vertebrate_mammalian, vertebrate_other (comma separated).
Only download genomes with the specified assembly level. Default: 'Complete Genome'.
Only download genomes in the specified refseq category. Default: any.
Only download the specified taxonomy IDs, comma separated. Default: any.
Download RNA sequences, too.
Filter unplaced sequences.
Mask low-complexity regions using dustmasker. Default: off.
Modify header to include taxonomy ID. Default: off.
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.

December 2017 centrifuge-download 1.0.3~beta