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'
- -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.