.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH SIMKAMIN_UPDATE "1" "September 2019" "simkaMin_update 1.5.1" "User Commands"
.SH NAME
simkaMin_update \- comparative metagenomics method dedicated to NGS datasets
.SH DESCRIPTION
.SS "[main options]:"
.TP
\fB\-in\fR
(1 arg) :    input file of datasets (datasets to add to existing simka results
.TP
\fB\-in\-to\-update\fR
(1 arg) :    path to existing simka results to update (existing results will be overwritten)
.TP
\fB\-bin\fR
(1 arg) :    path to simkaMinCore program (to be specified if not in PATH, or not in standard installation directory <simkaDir>/build/bin/simkaMinCore)
.SS "[core options]:"
.TP
\fB\-nb\-cores\fR
(1 arg) :    number of cores [Default: 0]
.TP
\fB\-max\-memory\fR
(1 arg) :    max memory (MB) [Default: 8000]
.SS "[k-mer options]:"
.TP
\fB\-filter\fR
(0 arg) :    filter out k\-mer seen one time (potentially erroneous)
.SS "[read options]:"
.TP
\fB\-max\-reads\fR
(1 arg) :    maximum number of reads per sample to process [Default: 0]
.TP
\fB\-min\-read\-size\fR
(1 arg) :    minimal size a read should have to be kept [Default: 0]
.TP
\fB\-min\-shannon\-index\fR
(1 arg) :    minimal Shannon index a read should have to be kept. Float in [0,2] [Default: 0]
.SH AUTHOR
This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.