genometools

Biostatistics
Genetics

Software Description

1

Info

Module Name

genometools

Last Updated On

08/29/2023

Support Level

Secondary Support

Software Access Level

Open Access

Home Page

http://genometools.org

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