table of contents
| CENTRIFUGE-DOWNLOAD(1) | User Commands | CENTRIFUGE-DOWNLOAD(1) |
NAME¶
centrifuge-download - centrifuge helper to download databases
DESCRIPTION¶
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.
AUTHOR¶
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 |