simkaMin - 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 1.5.1                                   September 2019                                      SIMKAMIN(1)

[mainoptions]:-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)

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

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

   [k-meroptions]:-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)

   [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 - comparative metagenomics method dedicated to NGS datasets