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fsm-lite - Frequency-based String Mining

FSM-LITE(1) User Commands FSM-LITE(1)

NAME

fsm-lite - Frequency-based String Mining

SYNOPSIS

fsm-lite -l <file> -t <file> [options]

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.

OPTIONS

mandatory:

-l,--list <file>
Text file that lists all input files as whitespace-separated pairs
<data-name> <data-filename>
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).
-t,--tmp <file>
Store temporary index data

optional:

-m,--min <int>
Minimum length to report (default 9)
-M,--max <int>
Maximum length to report (default 100)
-f,--freq <int>
Minimum frequency per input file to report (default 1)
-s,--minsupp <int>
Minimum number of input files with support to report (default 2)
-S,--maxsupp <int>
Maximum number of input files with support to report (default inf)
-v,--verbose
Verbose output

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
April 2016 fsm-lite 0.0+20151109