obisilva - description of obisilva
obisilva: 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.
- -s, --ssu
Specify that you are interested in the SSU
database.
Example:
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:
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.
- --DEBUG
- Sets logging in debug mode.
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