NAME

       simkaMin - comparative metagenomics method dedicated to NGS datasets

DESCRIPTION

   [main options]:
       -in    (1 arg) :    input file of datasets. One sample per line: id1: filename1...

       -out   (1 arg) :    output directory for result files (distance matrices) [Default: ./simka_results]

       -seed  (1 arg) :    seed used for random k-mer selection [Default: 100]

       -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]:
       -kmer-size
              (1 arg) :    size of a kmer [Default: 21]

       -nb-kmers
              (1 arg) :    number of kmers used to compute distances [Default: 1000000]

       -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.