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.