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.