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PanTools version 3

PanTools is a pangenomic toolkit for comparative analysis of large number of genomes. It is developed in the Bioinformatics Group of Wageningen University, the Netherlands. Please cite the relevant publication(s) from the list of publications if you use PanTools in your research.

Licence

PanTools has been licensed under GNU GENERAL PUBLIC LICENSE version 3.

Publications

Functionalities

PanTools currently provides these functionalities:

  • Construction of a pangenome
  • Construction of a panproteome
  • Adding new genomes to the pangenome
  • Adding structural annotations to the genomes
  • Detecting homology groups based on similarity of proteins
  • Retrieving features/regions/genomes
  • Read mappping
  • Gene classification
  • Functional annotation incorporation
  • Phylogenetic methods
  • Optimal homology grouping using BUSCO

Documentation

An extensive manual is available at https://pantools.readthedocs.io/.

Installation

First, clone this git and optionally checkout a release (please check the README.md file for specific installation instructions).

git clone https://git.wur.nl/bioinformatics/pantools.git
cd pantools

We provide conda environments for installing all dependencies of PanTools, which can be installed using conda/mamba (we recommend using mamba):

mamba env create -n pantools -f conda_linux.yml # for linux
mamba env create -n pantools -f conda_macos.yml # for macOS (does not include busco)

To build a standalone jar that can be run on any machine with a compatible JVM without any dependencies, install Maven and JDK version 8 (can also be installed via conda above). For compiling, run:

mvn package

mvn package will generate two jar files in the target/ directory. The standalone jar file is named pantools-<version>.jar, with <version> being the PanTools version you have checked out. To run it, use:

java -jar target/pantools-<version>.jar -h

Finally, we recommend making use of an alias to make running PanTools easier. For example, add the following to your ~/.bashrc file:

alias pantools="java -jar <path/to/pantools>/target/pantools-<version>.jar"

where <path/to/pantools> is the path to the directory where you checked out PanTools. Then, you can run PanTools by simply typing pantools in your terminal.

Contact

Should you have any questions or issues concerning PanTools, please contact us at pantools@bioinformatics.nl.