SIMKAMIN_UPDATE

NAME

simkaMin_update - comparative metagenomics method dedicated to NGS datasets

DESCRIPTION

[main options]:

-in

(1 arg) : input file of datasets (datasets to add to existing simka results

-in-to-update

(1 arg) : path to existing simka results to update (existing results will be overwritten)

-bin

(1 arg) : path to simkaMinCore program (to be specified if not in PATH, or not in standard installation directory <simkaDir>/build/bin/simkaMinCore)

[core options]:

-nb-cores

(1 arg) : number of cores [Default: 0]

-max-memory

(1 arg) : max memory (MB) [Default: 8000]

[k-mer options]:

-filter

(0 arg) : filter out k-mer seen one time (potentially erroneous)

[read options]:

-max-reads

(1 arg) : maximum number of reads per sample to process [Default: 0]

-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]

AUTHOR

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