GenomeTools

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Last Updated On: 

Tuesday, August 29, 2023

Support Level: 
Secondary Support
Software Access Level: 
Open Access
Home Page: 
Link
Software Categories: 
Biostatistics
Genetics
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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.

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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 <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

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.