Pantools
Description
PanTools is a toolkit for comparative analysis of large number of genomes, providing the following functionalities:
- Construction of a panproteome
- Adding new genomes to the pangenome
- Adding structural/functional annotations to the genomes
- Detecting homology groups based on similarity of proteins
- Optimization of homology grouping using BUSCO
- Read mapping
- Gene classification
- Phylogenetic methods
Environment Modules
Run module spider pantools to find out what environment modules are available for this application.
System Variables
- HPC_PANTOOLS_DIR - installation directory
- HPC_PANTOOLS_BIN - executables directory
Citation
If you publish research that uses pantools you have to cite it as follows:
Eef M Jonkheer, Dirk-Jan M van Workum, Siavash Sheikhizadeh Anari, Balázs Brankovics, Jorn R de Haan, Lidija Berke, Theo A J van der Lee, Dick de Ridder, Sandra Smit, PanTools v3: functional annotation, classification and phylogenomics, Bioinformatics, Volume 38, Issue 18, September 2022, Pages 4403–4405, https://doi.org/10.1093/bioinformatics/btac506
Jonkheer, E.M., Brankovics, B., Houwers, I.M. et al. The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool. BMC Genomics 22, 265 (2021). https://doi.org/10.1186/s12864-021-07583-5
Siavash Sheikhizadeh Anari, Dick de Ridder, M. Eric Schranz, Sandra Smit. Pangenomic read mapping.
bioRxiv 813634; doi: https://doi.org/10.1101/813634
Sheikhizadeh Anari, S., de Ridder, D., Schranz, M.E. et al. Efficient inference of homologs in large eukaryotic pan-proteomes. BMC Bioinformatics 19, 340 (2018). https://doi.org/10.1186/s12859-018-2362-4
Siavash Sheikhizadeh, M. Eric Schranz, Mehmet Akdel, Dick de Ridder, Sandra Smit, PanTools: representation, storage and exploration of pan-genomic data, Bioinformatics, Volume 32, Issue 17, September 2016, Pages i487–i493, https://doi.org/10.1093/bioinformatics/btw455