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OBISILVA(1) | OBITools | OBISILVA(1) |
NAME¶
obisilva - description of obisilvaobisilva: converts and optionally download the Silva database into an ecoPCR database. The formated database include the taxonomy as defined by the Silva authors.
WARNING:
Take care that the numeric taxids associated to the
sequences are specific to this Silva database and not compatible with the NCBI
taxids. The taxids present in a version of the Silva database (i.e ssu,
lsu, parc, ref…) are are just valid for this version of the database
and not compatible with the taxids used in another version.
OBISILVA SPECIFIC OPTIONS¶
- -s, --ssu
Specify that you are interested in the SSU
database.
Example:
> obisilva --ssu --parc
This download and format into an ecoPCR database the latest version of the SSUParc database of Silva.
- -l, --lsu
Specify that you are interested in the LSU
database.
Example:
> obisilva --ssu --parc
This download and format into an ecoPCR database the latest version of the LSUParc database of Silva.
- -p, --parc
- Specify that you are interested in the Parc (complete) version of the Silva database.
- -r, --ref
- Specify that you are interested in the Reference (cleaned to keep only high quality sequences) version of the Silva database.
- -n, --nr
- Specify that you are interested in the Non redundant version of the
Silva database. just a version of the to closely related sequence
is kept in this version of the database
WARNING:
Non redundant version of Silva exists only for the
SSU sequences in its Reference and Truncated version
- -t, --trunc
- Specify that you are interested in the Truncated (limited to the rDNA element without flanked regions) version of the Silva database.
- --local=<DIRNAME>
Specify you have already downloaded a copy of the
Silva database located at the following URL
http://www.arb-**Silva**.de/no_cache/download/archive/current/Exports/
Example:
> obisilva --ssu --parc --local=**Silva**Dir
This format the SSUParc version of the Silva database pre-downloaded in the **Silva**Dir directory.
COMMON OPTIONS¶
- -h, --help
- Shows this help message and exits.
- --DEBUG
- Sets logging in debug mode.
AUTHOR¶
The OBITools Development Team - LECACOPYRIGHT¶
2019 - 2015, OBITool Development TeamJanuary 28, 2019 | 1.02 12 |