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OBISILVA(1) OBITools OBISILVA(1)

NAME

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.


OBISILVA SPECIFIC OPTIONS

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.




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.




Specify that you are interested in the Parc (complete) version of the Silva database.

Specify that you are interested in the Reference (cleaned to keep only high quality sequences) version of the Silva database.

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



Specify that you are interested in the Truncated (limited to the rDNA element without flanked regions) version of the Silva database.

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

Shows this help message and exits.

Sets logging in debug mode.

AUTHOR

The OBITools Development Team - LECA

COPYRIGHT

2019 - 2015, OBITool Development Team

January 28, 2019 1.02 12