.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH SALMID "1" "December 2018" "SalmID 0.1.23" "User Commands"
.SH NAME
SalmID \- rapid Kmer based Salmonella identifier from sequence data
.SH SYNOPSIS
.B SalmID
[\-h] [\-v] [\-i your_fastqgz] [\-e file_extension] [\-d directory]
[\-r percentage, coverage or taxonomy] [\-m quick or thorough]
.SH DESCRIPTION
SalmID enables rapid confirmation of Salmonella spp. and subspp. from
sequence data.  This is done by checking taxonomic ID of single isolate
samples.  Currently only IDs Salmonella species and subspecies, and
some common contaminants (Listeria, Escherichia).
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-v\fR, \fB\-\-version\fR
show program's version number and exit
.TP
\fB\-i\fR your_fastqgz, \fB\-\-input_file\fR your_fastqgz
Single fastq.gz file input, include path to file if
file is not in same directory
.TP
\fB\-e\fR file_extension, \fB\-\-extension\fR file_extension
File extension, if specified without "\-\-input_dir",
SalmID will attempt to ID all files with this
extension in current directory, otherwise files in
input directory
.TP
\fB\-d\fR directory, \fB\-\-input_dir\fR directory
Directory which contains data for identification, when
not specified files in current directory will be
analyzed.
.TP
\fB\-r\fR percentage, coverage or taxonomy, \fB\-\-report\fR percentage, coverage or taxonomy
Report either percentage ("percentage") of clade
specific kmers recovered, average kmer\-coverage
("cov"), or taxonomy (taxonomic species ID, plus
observed mean k\-mer coverages and expected coverage).
.TP
\fB\-m\fR quick or thorough, \fB\-\-mode\fR quick or thorough
Quick [quick] or thorough [thorough] mode
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.