fsm-lite(1)

Usage

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

Overview

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

Releases

Unchanged in 5 releases since Debian 9 (Stretch).

9–13