genometools

Summary

  • Module Name: genometools

  • Support Level: Secondary Support

  • Software Access Level: Open Access

  • Home Page: 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.