obisilva1

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:

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.

Options

-h, --help: Shows this help message and exits.

--DEBUG: Sets logging in debug mode.