table of contents
| 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 |