---
name: "fsm-lite"
section: "1"
platform: "linux"
package: "fsm-lite"
version: "1.0-8"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fsm-lite"
---

# fsm-lite(1)

Frequency-based String Mining

## 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.