CENTRIFUGE-DOWNLOAD

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’. 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.

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.