simka - comparative metagenomics method dedicated to NGS
datasets
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 '']
This manpage was written by Shayan Doust for the Debian
distribution and can be used for any other usage of the program.