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.
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 <input_commands> 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
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.