.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH BACTERIA_TRADIS "1" "March 2017" "bacteria_tradis 1.3.1" "User Commands"
.SH NAME
bacteria_tradis \- bio-tradis: run a TraDIS analysis
.SH SYNOPSIS
.B bacteria_tradis
[\fI\,options\/\fR]
.SH DESCRIPTION
Run a TraDIS analysis. This involves:
1: filtering the data with tags matching that passed via \fB\-t\fR option
2: removing the tags from the sequences
3: mapping
4: creating an insertion site plot
5: creating a stats summary
.SH OPTIONS
.TP
\fB\-f\fR
text file listing fastq files with tradis tags attached
.TP
\fB\-t\fR
tag to search for
.TP
\fB\-r\fR
reference genome in fasta format (.fa)
.TP
\fB\-td\fR
tag direction \- 3 or 5 (optional. default = 3)
.TP
\fB\-mm\fR
number of mismatches allowed when matching tag (optional. default = 0)
.TP
\fB\-m\fR
mapping quality cutoff score (optional. default = 30)
.TP
\fB\-\-smalt_k\fR
custom k\-mer value for SMALT mapping (optional)
.TP
\fB\-\-smalt_s\fR
custom step size for SMALT mapping (optional)
.TP
\fB\-\-smalt_y\fR
custom y parameter for SMALT (optional. default = 0.96)
.TP
\fB\-\-smalt_r\fR
custom r parameter for SMALT (optional. default = \fB\-1\fR)
.TP
\fB\-n\fR
number of threads to use for SMALT and samtools sort (optional. default = 1)
.TP
\fB\-e\fR
set defaults for essentiality experiment (smalt_r = 0, \fB\-m\fR = 0)
.TP
\fB\-v\fR
verbose debugging output
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.