fsm-lite - Frequency-based String Mining
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.
- -l,--list <file>
- Text file that lists all input files as
- <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
- -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
- -S,--maxsupp <int>
- Maximum number of input files with support to report
- Verbose output
This manpage was written by Andreas Tille for the Debian distribution and can be
used for any other usage of the program.