centrifuge-download1
Centrifuge helper to download databases
Overview
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'. Use 'Any' for any assembly level.
-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.
Releases
4 releases since Debian 10 (Buster); the text changed 1 time.