.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH SIMKACOUNT "1" "September 2019" "simkaCount 1.5.1" "User Commands"
.SH NAME
simkaCount \- comparative metagenomics method dedicated to NGS datasets
.SH DESCRIPTION
ERROR: Unknown parameter '\-h'
ERROR: Option '\-out\-tmp\-simka' is mandatory
ERROR: Option '\-bank\-name' is mandatory
ERROR: Option '\-bank\-index' is mandatory
ERROR: Option '\-min\-read\-size' is mandatory
ERROR: Option '\-min\-shannon\-index' is mandatory
ERROR: Option '\-max\-reads' is mandatory
ERROR: Option '\-nb\-datasets' is mandatory
ERROR: Option '\-nb\-partitions' is mandatory
ERROR: Option '\-in' is mandatory
.PP
[SimkaCount options]
.TP
\fB\-nb\-cores\fR
(1 arg) :    number of cores  [default '0']
.TP
\fB\-verbose\fR
(1 arg) :    verbosity level  [default '1']
.TP
\fB\-version\fR
(0 arg) :    version
.TP
\fB\-help\fR
(0 arg) :    help
.TP
\fB\-out\-tmp\-simka\fR
(1 arg) :    tmp output
.TP
\fB\-bank\-name\fR
(1 arg) :    bank name
.TP
\fB\-bank\-index\fR
(1 arg) :    bank name
.TP
\fB\-min\-read\-size\fR
(1 arg) :    bank name
.TP
\fB\-min\-shannon\-index\fR
(1 arg) :    bank name
.TP
\fB\-max\-reads\fR
(1 arg) :    bank name
.TP
\fB\-nb\-datasets\fR
(1 arg) :    bank name
.TP
\fB\-nb\-partitions\fR
(1 arg) :    bank name
.TP
\fB\-in\fR
(1 arg) :    reads file
.TP
\fB\-kmer\-size\fR
(1 arg) :    size of a kmer  [default '31']
.TP
\fB\-abundance\-min\fR
(1 arg) :    min abundance threshold for solid kmers  [default '0']
.TP
\fB\-abundance\-max\fR
(1 arg) :    max abundance threshold for solid kmers  [default '2147483647']
.TP
\fB\-abundance\-min\-threshold\fR
(1 arg) :    min abundance hard threshold (only used when min abundance is "auto")  [default '2']
.TP
\fB\-histo\-max\fR
(1 arg) :    max number of values in kmers histogram  [default '10000']
.TP
\fB\-solidity\-kind\fR
(1 arg) :    way to compute counts of several files (sum, min, max, one, all, custom)  [default 'sum']
.TP
\fB\-solidity\-custom\fR
(1 arg) :    when solidity\-kind is custom, specifies list of files where kmer must be present  [default '']
.TP
\fB\-max\-memory\fR
(1 arg) :    max memory (in MBytes)  [default '5000']
.TP
\fB\-max\-disk\fR
(1 arg) :    max disk   (in MBytes)  [default '0']
.TP
\fB\-solid\-kmers\-out\fR
(1 arg) :    output file for solid kmers (only when constructing a graph)  [default '']
.TP
\fB\-out\fR
(1 arg) :    output file  [default '']
.TP
\fB\-out\-dir\fR
(1 arg) :    output directory  [default '.']
.TP
\fB\-out\-tmp\fR
(1 arg) :    output directory for temporary files  [default '.']
.TP
\fB\-out\-compress\fR
(1 arg) :    h5 compression level (0:none, 9:best)  [default '0']
.TP
\fB\-storage\-type\fR
(1 arg) :    storage type of kmer counts ('hdf5' or 'file')  [default 'hdf5']
.TP
\fB\-histo2D\fR
(1 arg) :    compute the 2D histogram (with first file = genome, remaining files = reads)  [default '0']
.TP
\fB\-histo\fR
(1 arg) :    output the kmer abundance histogram  [default '0']
.IP
[kmer count, advanced performance tweaks options]
.TP
\fB\-minimizer\-type\fR
(1 arg) :    minimizer type (0=lexi, 1=freq)  [default '0']
.TP
\fB\-minimizer\-size\fR
(1 arg) :    size of a minimizer  [default '10']
.TP
\fB\-repartition\-type\fR (1 arg) :
minimizer repartition (0=unordered, 1=ordered)  [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.