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.