.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH SIMKA "1" "September 2019" "simka 1.5.1" "User Commands"
.SH NAME
simka \- comparative metagenomics method dedicated to NGS datasets
.SH DESCRIPTION
ERROR: Unknown parameter '\-h'
ERROR: Option '\-in' is mandatory
ERROR: Option '\-out\-tmp' is mandatory
ERROR: Option '\-in' is mandatory
.PP
[Simka options]
.TP
\fB\-in\fR
(1 arg) :    input file of samples. One sample per line: id1: filename1...
.TP
\fB\-out\fR
(1 arg) :    output directory for result files (distance matrices)  [default './simka_results']
.TP
\fB\-out\-tmp\fR
(1 arg) :    output directory for temporary files
.TP
\fB\-keep\-tmp\fR
(0 arg) :    keep temporary files
.TP
\fB\-data\-info\fR (0 arg) :
compute (and display) information before running Simka, such as the number of reads per dataset
.TP
\fB\-verbose\fR
(1 arg) :    verbosity level  [default '1']
.TP
\fB\-version\fR
(0 arg) :    version
.TP
\fB\-help\fR
(0 arg) :    help
.IP
[distance options]
.TP
\fB\-simple\-dist\fR
(0 arg) :    compute all simple distances (Chord, Hellinger...)
.TP
\fB\-complex\-dist\fR (0 arg) :
compute all complex distances (Jensen\-Shannon...)
.IP
[kmer options]
.TP
\fB\-kmer\-size\fR
(1 arg) :    size of a kmer  [default '21']
.TP
\fB\-abundance\-min\fR
(1 arg) :    min abundance a kmer need to be considered  [default '2']
.TP
\fB\-abundance\-max\fR
(1 arg) :    max abundance a kmer can have to be considered  [default '999999999']
.TP
\fB\-kmer\-shannon\-index\fR (1 arg) :
minimal Shannon index a kmer should have to be kept. Float in [0,2]  [default '0']
.IP
[read options]
.TP
\fB\-max\-reads\fR
(1 arg) :    maximum number of reads per sample to process. Can be \fB\-1\fR: use all reads. Can be 0: estimate it  [default '\-1']
.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']
.IP
[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 '5000']
.TP
\fB\-max\-count\fR
(1 arg) :    maximum number of simultaneous counting jobs (a higher value improve execution time but increase temporary disk usage)  [default '']
.TP
\fB\-max\-merge\fR
(1 arg) :    maximum number of simultaneous merging jobs (1 job = 1 core)  [default '']
.IP
[cluster options]
.TP
\fB\-count\-cmd\fR
(1 arg) :    command to submit counting job  [default '']
.TP
\fB\-merge\-cmd\fR
(1 arg) :    command to submit merging job  [default '']
.TP
\fB\-count\-file\fR (1 arg) :
filename to the couting job template  [default '']
.TP
\fB\-merge\-file\fR (1 arg) :
filename to the merging job template  [default '']
.SH AUTHOR
This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.