PanTools version 4

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

• PanTools: representation, storage and exploration of pan-genomic data.
• Efficient inference of homologs in large eukaryotic pan-proteomes.
• Pan-genomic read mapping
• The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool.
• PanTools v3: functional annotation, classification, and phylogenomics

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 mapping
• Gene classification
• Functional annotation incorporation
• Phylogenetic methods
• Optimal homology grouping using BUSCO

Documentation

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

Cloning this git

For cloning this git, please run:

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

And check out a desired version (e.g. v4.0.0):

git checkout v4.0.0

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)

Building a runnable jar

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. Then run mvn package in the PanTools root directory:

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 (we'll take version v4.0.0 as an example):

java -jar target/pantools-4.0.0.jar

Contact

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