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.

Publications

• [2022] PanTools v3: functional annotation, classification, and phylogenomics
• [2021] The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool.
• [2019] Pan-genomic read mapping
• [2018] Efficient inference of homologs in large eukaryotic pan-proteomes.
• [2016] PanTools: representation, storage and exploration of pan-genomic data.

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.yaml

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.

Licence

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

Copyright (C) 2016  the PanTools team, Bioinformatics Group, Wageningen University & Research

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.