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

       -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 - LECA

COPYRIGHT

       2019 - 2015, OBITool Development Team

 1.02 12                                   Jan 28, 2019                               OBISILVA(1)