.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH PLASMIDSEEKER "1" "October 2018" "plasmidseeker 1.0" "User Commands"
.SH NAME
plasmidseeker \- identification of known plasmids from whole-genome sequencing reads
.SH SYNOPSIS
.B plasmidseeker
\fI\,-d <PLASMID DB DIR> -i <SAMPLE.fastq> -b <CLOSEST BACTERIA TO ISOLATE> -o <OUTPUT FILE>\/\fR
.SH OPTIONS
.TP
\fB\-i\fR
Input fastq file
.TP
\fB\-o\fR
Output file name (default plasmidseeker_result.txt)
.TP
\fB\-d\fR
Path to plasmid database directory
.TP
\fB\-b\fR
Closest bacteria to isolate genome fna
.TP
\fB\-t\fR
Number of threads used (default 32)
.TP
\fB\-f\fR
Minimum threshold F \- at least this fraction of unique k\-mers that has to be found for a plasmid (default 80)
.TP
\fB\-h\fR
Print this help
.TP
\fB\-\-verbose\fR
Print out more working process
.TP
\fB\-\-ponly\fR
Assumes that reads contain only plasmid sequences (use for extracted plasmids)
.TP
\fB\-v\fR
Print version of the program
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.