# genometools

## Summary

+ **Module Name:** genometools
+ **Support Level:** Secondary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [http://genometools.org](http://genometools.org)

## Software Description

The GenomeTools genome analysis system is a free collection of
bioinformatics tools (in the realm of genome informatics) combined into
a single binary. It is based on a C library named "libgenometools" which
consists of several modules.
## General Linux

To load this software in a Linux environment run the commands:

	module load genometools

To use a software tool contained in GenomeTools, such as LTRharvest,
enter the command:

	gt ltrharvest <input_commands>

Here ltrharvest is used as an example of one possible software tool, and
stands for the appropriate input commands the user has chosen for use
with the tool. To obtain a list of all tools in GenomeTools, enter the
command

	gt -help

The individual tools implement a -help option. For example, to learn the
options accepted by LTRharvest, enter the command:

	gt ltrharvest -help

The software tools included in GenomeTools are:

- **ltrharvest** - an efficient and flexible software tool for de novo detection of LTR retrotransposons.
- **tallymer** - a collection of flexible and memory-efficient programs for k-mer counting and indexing of large sequence sets.
- **uniquesub** - a program for computing minimum unique substrings.
- **AnnotationSketch** - a library for drawing genome annotations.
- **ltrdigest** - a software tool for automated annotation of internal features of LTR retrotransposons.
- **MetaGenomeThreader** - a software to predict genes, such as PCS\'s (predicted coding sequences) in sequences of metagenome projects.
- **GtEncseq** - a compressed biosequence representation with many features.
- **Readjoiner** - a sequence assembler based on the assembly string graph framework.

GenomeTools is freely availabe at <http://genometools.org/> .  This
website also contains information on the included software tools and
their use.