NAME

       simka - comparative metagenomics method dedicated to NGS datasets

DESCRIPTION

       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 '']

AUTHOR

       This  manpage  was written by Shayan Doust for the Debian distribution and can be used for
       any other usage of the program.