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.