NAME

       simkaCount - comparative metagenomics method dedicated to NGS datasets

DESCRIPTION

       ERROR:  Unknown  parameter  '-h' ERROR: Option '-out-tmp-simka' is mandatory ERROR: Option
       '-bank-name'  is  mandatory  ERROR:  Option  '-bank-index'  is  mandatory  ERROR:   Option
       '-min-read-size'  is  mandatory  ERROR:  Option  '-min-shannon-index'  is mandatory ERROR:
       Option '-max-reads' is mandatory ERROR: Option '-nb-datasets' is mandatory  ERROR:  Option
       '-nb-partitions' is mandatory ERROR: Option '-in' is mandatory

       [SimkaCount options]

       -nb-cores
              (1 arg) :    number of cores  [default '0']

       -verbose
              (1 arg) :    verbosity level  [default '1']

       -version
              (0 arg) :    version

       -help  (0 arg) :    help

       -out-tmp-simka
              (1 arg) :    tmp output

       -bank-name
              (1 arg) :    bank name

       -bank-index
              (1 arg) :    bank name

       -min-read-size
              (1 arg) :    bank name

       -min-shannon-index
              (1 arg) :    bank name

       -max-reads
              (1 arg) :    bank name

       -nb-datasets
              (1 arg) :    bank name

       -nb-partitions
              (1 arg) :    bank name

       -in    (1 arg) :    reads file

       -kmer-size
              (1 arg) :    size of a kmer  [default '31']

       -abundance-min
              (1 arg) :    min abundance threshold for solid kmers  [default '0']

       -abundance-max
              (1 arg) :    max abundance threshold for solid kmers  [default '2147483647']

       -abundance-min-threshold
              (1  arg) :    min abundance hard threshold (only used when min abundance is "auto")
              [default '2']

       -histo-max
              (1 arg) :    max number of values in kmers histogram  [default '10000']

       -solidity-kind
              (1 arg) :    way to compute counts of several  files  (sum,  min,  max,  one,  all,
              custom)  [default 'sum']

       -solidity-custom
              (1  arg) :    when solidity-kind is custom, specifies list of files where kmer must
              be present  [default '']

       -max-memory
              (1 arg) :    max memory (in MBytes)  [default '5000']

       -max-disk
              (1 arg) :    max disk   (in MBytes)  [default '0']

       -solid-kmers-out
              (1 arg) :    output file for solid kmers (only when constructing a graph)  [default
              '']

       -out   (1 arg) :    output file  [default '']

       -out-dir
              (1 arg) :    output directory  [default '.']

       -out-tmp
              (1 arg) :    output directory for temporary files  [default '.']

       -out-compress
              (1 arg) :    h5 compression level (0:none, 9:best)  [default '0']

       -storage-type
              (1 arg) :    storage type of kmer counts ('hdf5' or 'file')  [default 'hdf5']

       -histo2D
              (1  arg) :    compute the 2D histogram (with first file = genome, remaining files =
              reads)  [default '0']

       -histo (1 arg) :    output the kmer abundance histogram  [default '0']

              [kmer count, advanced performance tweaks options]

       -minimizer-type
              (1 arg) :    minimizer type (0=lexi, 1=freq)  [default '0']

       -minimizer-size
              (1 arg) :    size of a minimizer  [default '10']

       -repartition-type (1 arg) :
              minimizer repartition (0=unordered, 1=ordered)  [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.