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
- 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.
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
Cloning this git
For cloning this git, please run:
git clone --recursive https://git.wur.nl/bioinformatics/pantools.git
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 3.3.3
as an example):
java -jar target/pantools-3.3.3.jar
Requirements, Installation, Usage
An extensive manual is available at http://www.bioinformatics.nl/pangenomics/manual/
To use the consensus_tree
functionality, PanTools depends on ASTER. For compiling this submodule, please run:
cd ASTER
g++ -std=gnu++11 -march=native -Ofast -pthread astral.cpp -o astral
g++ -std=gnu++11 -march=native -Ofast -pthread astral-pro.cpp -o astral-pro
In case the directory pantools/ASTER is empty, please run the following to retrieve its contents:
git submodule update --init --recursive