PanTools-pipeline-v4
PA
General purpose Snakemake pipeline for PanTools v4.
Updated 8 months ago
5
Get started
2324 commitsLast commit ≈ 6 days ago5 stars6 forks
Ctrl K
PanTools
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.
29
mentions
3
contributors
What PanTools can do for you
PanTools currently provides these 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
Keywords
Programming languages
License
</>Source code
Packages
Participating organisations
Reference papers
Mentions
Conference papers
2- 1.Author(s): Jérôme Arnoux, Angela Bonifati, Alexandra Calteau, Stefania Dumbrava, Guillaume GautreauPublished in 2024 IEEE 40th International Conference on Data Engineering Workshops (ICDEW) by IEEE in 2024, page: 350-35410.1109/icdew61823.2024.00052
- 2.Author(s): Yifan Li, Giulia GuidiPublished in Proceedings of the 53rd International Conference on Parallel Processing by ACM in 2024, page: 919-92810.1145/3673038.3673072
Journal articles
12- 1.Author(s): Guohui Shi, Yi Dai, Da Zhou, Mengmeng Chen, Jiaqi Zhang, Yilong Bi, Shuai Liu, Qi WuPublished in Mycology by Informa UK Limited in 2024, page: 1-1510.1080/21501203.2024.2358868
- 2.Author(s): Francesco Garassino, Sofia Bengoa Luoni, Tommaso Cumerlato, Francisca Reyes Marquez, Jeremy Harbinson, Mark G M Aarts, Harm Nijveen, Sandra SmitPublished in G3: Genes, Genomes, Genetics by Oxford University Press (OUP) in 202410.1093/g3journal/jkae175
- 3.Author(s): Yael Tirlet, Matéo Boudet, Emmanuelle Becker, Fabrice Legeai, Olivier DameronPublished in 202410.1016/j.csbj.2024.11.022
- 4.Author(s): Vincenzo Bonnici, Davide ChiccoPublished in BioData Mining by Springer Science and Business Media LLC in 202410.1186/s13040-024-00380-2
- 5.Author(s): Dirk-Jan M. van Workum, Sarah L. Mehrem, Basten L. Snoek, Marrit C. Alderkamp, Dmitry Lapin, Flip F. M. Mulder, Guido Van den Ackerveken, Dick de Ridder, M. Eric Schranz, Sandra SmitPublished in BMC Plant Biology by Springer Science and Business Media LLC in 202410.1186/s12870-024-05712-2
- 6.Author(s): David C. Rinker, Thomas J. C. Sauters, Karin Steffen, Adiyantara Gumilang, Huzefa A. Raja, Manuel Rangel-Grimaldo, Camila Figueiredo Pinzan, Patrícia Alves de Castro, Thaila Fernanda dos Reis, Endrews Delbaje, Jos Houbraken, Gustavo H. Goldman, Nicholas H. Oberlies, Antonis RokasPublished in Communications Biology by Springer Science and Business Media LLC in 202410.1038/s42003-024-06756-8
- 7.Author(s): Meixin Yang, Sandra Smit, Dick de Ridder, Jie Feng, Taiguo Liu, Jinrong Xu, Theo A. J. van der Lee, Hao Zhang, Wanquan ChenPublished in Advanced Science by Wiley in 202410.1002/advs.202401899
- 8.Author(s): Samuel T. Horsfield, Gerry Tonkin-Hill, Nicholas J. Croucher, John A. LeesPublished in Genome Research by Cold Spring Harbor Laboratory in 2023, page: 1622-163710.1101/gr.277733.123
- 9.Author(s): Anthony J Aylward, Semar Petrus, Allen Mamerto, Nolan T Hartwick, Todd P MichaelPublished in Bioinformatics by Oxford University Press (OUP) in 202310.1093/bioinformatics/btad621
- 10.Author(s): Theo A. J. van der Lee, Marga P. E. van Gent-Pelzer, Eef M. Jonkheer, Balázs Brankovics, Ilse M. Houwers, Jan M. van der Wolf, Peter J. M. Bonants, Inge van Duivenbode, Robert A. M. Vreeburg, Mathijs Nas, Sandra SmitPublished in Microorganisms by MDPI AG in 2023, page: 208010.3390/microorganisms11082080
- 11.Author(s): Sushma Naithani, Cecilia H. Deng, Sunil Kumar Sahu, Pankaj JaiswalPublished in Biomolecules by MDPI AG in 2023, page: 140310.3390/biom13091403
- 12.Author(s): Wei Xiong, Dirk-Jan M van Workum, Lidija Berke, Linda V Bakker, Elio Schijlen, Frank F M Becker, Henri van de Geest, Sander Peters, Richard Michelmore, Rob van Treuren, Marieke Jeuken, Sandra Smit, M Eric SchranzPublished in G3: Genes, Genomes, Genetics by Oxford University Press (OUP) in 202310.1093/g3journal/jkad204
Thesis
2Other
12- 1.Author(s): Eef M. Jonkheer, Dick de Ridder, Theo A.J. van der Lee, Jorn R. de Haan, Lidija Berke, Sandra SmitPublished by Cold Spring Harbor Laboratory in 202410.1101/2024.06.05.597558
- 2.Author(s): Lakhansing A. Pardeshi, Inge van Duivenbode, Michiel J. C. Pel, Eef M. Jonkheer, Anne Kupczok, Dick de Ridder, Sandra Smit, Theo A. J. van der LeePublished by Cold Spring Harbor Laboratory in 202410.1101/2024.09.02.610764
- 3.Author(s): David C. Rinker, Thomas J. C. Sauters, Karin Steffen, Adiyantara Gumilang, Huzefa A. Raja, Manuel Rangel-Grimaldo, Camila Figueiredo Pinzan, Patrícia Alves de Castro, Thaila Fernanda dos Reis, Endrews Delbaje, Jos Houbraken, Gustavo H. Goldman, Nicholas H. Oberlies, Antonis RokasPublished by Cold Spring Harbor Laboratory in 202410.1101/2024.03.08.583994
- 4.Author(s): Thibault Leroy, Pierre Faux, Benjamin Basso, Sonia Eynard, David Wragg, Alain VignalPublished by Cold Spring Harbor Laboratory in 202410.1101/2024.09.04.611184
- 5.Author(s): Gaetan Droc, Delphine Giraud, Caroline Belser, Karine Labadie, Simone Duprat, Corinne Cruaud, Benjamin Istace, Fredson Dos Santos Menezes, Franck Curk, Gilles Costantino, Alexandre Soriano, Pierre Mournet, Alexis Dereeper, Maëva Miranda, Elodie Marchi, Sylvain Santoni, Raner Santana, Stéphanie Sidibe-Bocs, François Luro, Nathalie Choisne, Florian Maumus, Barbara Hufnagel, Fabienne Micheli, Patrick Wincker, Jean-Marc Aury, Arnaud Lemainque, Patrick OllitraultPublished in 202410.1101/2024.10.17.618847
- 6.Author(s): Dirk-Jan M. van Workum, Sarah L. Mehrem, Basten L. Snoek, Marrit C. Alderkamp, Dmitry Lapin, Flip F.M. Mulder, Guido Van den Ackerveken, Dick de Ridder, M. Eric Schranz, Sandra SmitPublished in 202410.1101/2024.06.20.599299
- 7.Author(s): Wei Xiong, Dirk-Jan M. van Workum, Lidija Berke, Linda V. Bakker, Elio Schijlen, Frank F.M. Becker, Henri van de Geest, Sander Peters, Richard Michelmore, Rob van Treuren, Marieke Jeuken, Sandra Smit, M. Eric SchranzPublished by Cold Spring Harbor Laboratory in 202310.1101/2023.05.03.539295
- 8.Author(s): Astrid van den Brandt, Eef Jonkheer, Dirk-Jan van Workum, Huub van de Wetering, Sandra Smit, Anna VilanovaPublished by Institute of Electrical and Electronics Engineers (IEEE) in 202310.36227/techrxiv.21572433.v2
- 9.Author(s): Francesco Garassino, Sofia Bengoa Luoni, Tommaso Cumerlato, Francisca Reyes Marquez, Jeremy Harbinson, Mark G. M. Aarts, Harm Nijveen, Sandra SmitPublished by Cold Spring Harbor Laboratory in 202310.1101/2023.10.18.562717
- 10.Author(s): Astrid van den Brandt, Eef Jonkheer, Dirk-Jan van Workum, Huub van de Wetering, Sandra Smit, Anna VilanovaPublished by Institute of Electrical and Electronics Engineers (IEEE) in 202310.36227/techrxiv.21572433
- 11.Author(s): Sushma Naithani, Cecilia H. Deng, Sunil Kumar Sahu, Pankaj JaiswalPublished by MDPI AG in 202310.20944/preprints202308.1641.v1
- 12.Author(s): Astrid van den Brandt, Eef Jonkheer, Dirk-Jan van Workum, Huub van de Wetering, Sandra Smit, Anna VilanovaPublished by Institute of Electrical and Electronics Engineers (IEEE) in 202210.36227/techrxiv.21572433.v1
Contributors
Contact person
SS
Thijs van Lankveld
EJ
Eef Jonkheer
SS
Sandra Smit
Related projects
Scaling up pangenomics for plant breeding
Delivering a pangenome approach that drastically improves the analytical power on plant data
Updated 6 months ago
Finished
Related software
PanVA
PA
Variant Analysis within Pangenomes.
Updated 8 months ago
2 2