simka - 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.

simka 1.5.1                                      September 2019                                         SIMKA(1)

       ERROR:  Unknown  parameter  '-h'  ERROR:  Option '-in' is mandatory ERROR: Option '-out-tmp' is mandatory
       ERROR: Option '-in' is mandatory

       [Simka options]

       -in    (1 arg) :    input file of samples. One sample per line: id1: filename1...

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

       -out-tmp
              (1 arg) :    output directory for temporary files

       -keep-tmp
              (0 arg) :    keep temporary files

       -data-info (0 arg) :
              compute (and display) information before running Simka, such as the number of reads per dataset

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

       -version
              (0 arg) :    version

       -help  (0 arg) :    help

              [distance options]

       -simple-dist
              (0 arg) :    compute all simple distances (Chord, Hellinger...)

       -complex-dist (0 arg) :
              compute all complex distances (Jensen-Shannon...)

              [kmer options]

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

       -abundance-min
              (1 arg) :    min abundance a kmer need to be considered  [default '2']

       -abundance-max
              (1 arg) :    max abundance a kmer can have to be considered  [default '999999999']

       -kmer-shannon-index (1 arg) :
              minimal Shannon index a kmer should have to be kept. Float in [0,2]  [default '0']

              [read options]

       -max-reads
              (1 arg) :    maximum number of reads per sample to process. Can be -1: use all reads.  Can  be  0:
              estimate it  [default '-1']

       -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']

              [core options]

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

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

       -max-count
              (1  arg)  :    maximum number of simultaneous counting jobs (a higher value improve execution time
              but increase temporary disk usage)  [default '']

       -max-merge
              (1 arg) :    maximum number of simultaneous merging jobs (1 job = 1 core)  [default '']

              [cluster options]

       -count-cmd
              (1 arg) :    command to submit counting job  [default '']

       -merge-cmd
              (1 arg) :    command to submit merging job  [default '']

       -count-file (1 arg) :
              filename to the couting job template  [default '']

       -merge-file (1 arg) :
              filename to the merging job template  [default '']

       simka - comparative metagenomics method dedicated to NGS datasets