.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
.TH FSM-LITE "1" "April 2016" "fsm-lite 0.0+20151109" "User Commands"
.SH NAME
fsm-lite \- Frequency-based String Mining
.SH SYNOPSIS
.B fsm\-lite
\fB\-l\fR <file> \fB\-t\fR <file> [options]
.SH DESCRIPTION
A singe-core implementation of frequency-based substring mining used in
bioinformatics to extract substrings that discriminate two (or more)
datasets inside high-throughput sequencing data.
.SH OPTIONS
.SS mandatory:
.TP
\fB\-l\fR,\-\-list <file>
Text file that lists all input files as whitespace\-separated pairs
.IP
<data\-name> <data\-filename>
.IP
where <data\-name> is unique identifier (without whitespace)
and <data\-filename> is full path to each input file.
Default data file format is FASTA (uncompressed).
.TP
\fB\-t\fR,\-\-tmp <file>
Store temporary index data
.SS "optional:"
.TP
\fB\-m\fR,\-\-min <int>
Minimum length to report (default 9)
.TP
\fB\-M\fR,\-\-max <int>
Maximum length to report (default 100)
.TP
\fB\-f\fR,\-\-freq <int>
Minimum frequency per input file to report (default 1)
.TP
\fB\-s\fR,\-\-minsupp <int>
Minimum number of input files with support to report (default 2)
.TP
\fB\-S\fR,\-\-maxsupp <int>
Maximum number of input files with support to report (default inf)
.TP
\fB\-v\fR,\-\-verbose
Verbose 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.