NAME

       simkaMin_update - comparative metagenomics method dedicated to NGS datasets

DESCRIPTION

   [main options]:
       -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)

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

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

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

   [read options]:
       -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]

AUTHOR

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