.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH SEQSERO "1" "April 2017" "seqsero 1.0" "User Commands"
.SH NAME
seqsero \- Salmonella serotyping from genome sequencing data
.SH SYNOPSIS
.B seqsero
\fB\-m\fR <data_type> \fB\-i\fR <input_data> [\-b <BWA_algorithm>]
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-m\fR {1,2,3,4}
<int>: '1'(pair\-end reads, interleaved),'2'(pair\-end reads,
seperated),'3'(single\-end reads), '4'(assembly)
.TP
\fB\-i\fR I [I ...]
<string>: path/to/input_data
.TP
\fB\-b\fR {sam,mem}
<string>: 'sam'(bwa samse/sampe), 'mem'(bwa mem), default=sam
.SH AUTHOR
SeqSero was developed by Shaokang Zhang (zskzsk@uga.edu) and Xiangyu Deng (xdeng@uga.edu)
.PP
Contact email:seqsero@gmail.com
.PP
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.