simkaCount - 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.

simkaCount 1.5.1                                 September 2019                                    SIMKACOUNT(1)

       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']

       simkaCount - comparative metagenomics method dedicated to NGS datasets