simkaMin_update - comparative metagenomics method dedicated to NGS datasets

       This manpage was written by Shayan Doust for the Debian distribution and can be used for any other  usage
       of the program.

simkaMin_update 1.5.1                            September 2019                               SIMKAMIN_UPDATE(1)

[mainoptions]:-in    (1 arg) :    input file of datasets (datasets to add to existing simka results

       -in-to-update
              (1 arg) :    path to existing simka results to update (existing results will be overwritten)

       -bin   (1  arg)  :     path  to  simkaMinCore program (to be specified if not in PATH, or not in standard
              installation directory <simkaDir>/build/bin/simkaMinCore)

   [coreoptions]:-nb-cores
              (1 arg) :    number of cores [Default: 0]

       -max-memory
              (1 arg) :    max memory (MB) [Default: 8000]

   [k-meroptions]:-filter
              (0 arg) :    filter out k-mer seen one time (potentially erroneous)

   [readoptions]:-max-reads
              (1 arg) :    maximum number of reads per sample to process [Default: 0]

       -min-read-size
              (1 arg) :    minimal size a read should have to be kept [Default: 0]

       -min-shannon-index
              (1 arg) :    minimal Shannon index a read should have to be kept. Float in [0,2] [Default: 0]

       simkaMin_update - comparative metagenomics method dedicated to NGS datasets