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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
.TH CENTRIFUGE-DOWNLOAD "1" "December 2017" "centrifuge-download 1.0.3~beta" "User Commands"
.SH NAME
centrifuge-download \- centrifuge helper to download databases
.SH DESCRIPTION
centrifuge\-download [<options>] <database>
.PP
ARGUMENT
.TP
<database>
One of refseq, genbank, contaminants or taxonomy:
.TP
\- use refseq or genbank for genomic sequences,
\- contaminants gets contaminant sequences from UniVec and EmVec,
\- taxonomy for taxonomy mappings.
.PP
COMMON OPTIONS
.TP
\fB\-o\fR <directory>
Folder to which the files are downloaded. Default: '.'.
.TP
\fB\-P\fR <# of threads>
Number of processes when downloading (uses xargs). Default: '1'
.SS "WHEN USING database refseq OR genbank:"
.TP
\fB\-d\fR <domain>
What domain to download. One or more of bacteria, viral, archaea, fungi, protozoa, invertebrate, plant, vertebrate_mammalian, vertebrate_other (comma separated).
.TP
\fB\-a\fR <assembly level>
Only download genomes with the specified assembly level. Default: 'Complete Genome'.
.TP
\fB\-c\fR <refseq category>
Only download genomes in the specified refseq category. Default: any.
.TP
\fB\-t\fR <taxids>
Only download the specified taxonomy IDs, comma separated. Default: any.
.TP
\fB\-r\fR
Download RNA sequences, too.
.TP
\fB\-u\fR
Filter unplaced sequences.
.TP
\fB\-m\fR
Mask low\-complexity regions using dustmasker. Default: off.
.TP
\fB\-l\fR
Modify header to include taxonomy ID. Default: off.
.TP
\fB\-g\fR
Download GI map.
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
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