genometools
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.
Info
Module Name
genometools
Last Updated On
08/29/2023
Support Level
Secondary Support
Software Access Level
Open Access
Home Page
Documentation
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.
Agate Modules
Default
1.5.9
Other Modules
1.5.9
Mangi Modules
Default
1.5.9
Other Modules
1.5.9
Mesabi Modules
Default
1.5.9
Other Modules
1.5.9