---
name: "centrifuge-download"
section: "1"
platform: "linux"
package: "centrifuge"
version: "1.0.4.2-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/centrifuge-download"
---

# centrifuge-download(1)

centrifuge helper to download databases

## 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.