PanTools-pipeline-v4
PA
General purpose Snakemake pipeline for PanTools v4.
Updated 19 months ago
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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.
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mentions
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contributors
Description
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
License
Packages
Participating organisations
Reference papers
Mentions
- 1.Author(s): Fatima Noor, Kinza Fatima, Muhammad Farukh, Muhammad Tahir ul QamarPublished in Plant Pangenomes and Pangenomics by Elsevier in 2025, page: 25-4810.1016/b978-0-443-26791-8.00002-9
- 2.Author(s): Latha-Devi Ananda-Lekshmi, Gunasekaran Ariharasutharsan, Mueen Alam Khan, Adhimoolam KarthikeyanPublished in Plant Pangenomes and Pangenomics by Elsevier in 2025, page: 385-40610.1016/b978-0-443-26791-8.00019-4
- 3.Author(s): Arushi Arora, Jatin Sharma, Sreya Venadan, Deepak Bhamare, Sourabh Kumar, Shubham Sharma, Mayank Pratap Singh Bangari, Dinesh Kumar SainiPublished in Plant Pangenomes and Pangenomics by Elsevier in 2025, page: 49-7410.1016/b978-0-443-26791-8.00003-0
- 4.Author(s): Stefanie Nachtweide, Lars Romoth, Mario StankePublished in Methods in Molecular Biology, Comparative Genomics by Springer US in 2024, page: 165-18710.1007/978-1-0716-3838-5_7
- 5.Author(s): Christina Papastolopoulou, Zijiang Yang, Dirk-Jan M. van Workum, Raúl Y. Wijfjes, Sandra SmitPublished in Methods in Molecular Biology, Genome Assembly by Springer US in 2012, page: 293-31610.1007/978-1-0716-4702-8_14
- 1.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
- 2.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
- 1.Author(s): Darien Deschner, Janet E. HillPublished in 202510.1371/journal.pone.0325338
- 2.Author(s): Marc C. Heuermann, Pedro Barros, Sebastian Beier, Heidrun Gundlach, Jorge Alvarez-Jarreta, Keywan Hassani-Pak, Patrick König, Anne Fiebig, Tim Godec, Kristina Gruden, Nadja Nolte, Marko Petek, Uwe Scholz, Maja Zagorščak, Klaas Vandepoele, Michiel Van BelPublished in F1000Research by F1000 Research Ltd in 2025, page: 73910.12688/f1000research.166538.1
- 3.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 in Microbial Genomics by Microbiology Society in 202510.1099/mgen.0.001392
- 4.Author(s): Eef M. Jonkheer, Dick de Ridder, Theo A. J. van der Lee, Jorn R. de Haan, Lidija Berke, Sandra SmitPublished in Plant Biotechnology Journal by Wiley in 2025, page: 874-88610.1111/pbi.14545
- 5.Author(s): Adam P. Ryan, Sean Bergin, Jillian Scully, Evelyn Zuniga-Soto, Conor Hession, Amelia E. Barber, Emilia Gómez-Molero, Oliver Bader, Florent Morio, Bing Zhai, Kenneth H. Wolfe, Geraldine ButlerPublished in mBio by American Society for Microbiology in 202510.1128/mbio.01320-25
- 6.Author(s): A. van den Brandt, E. Ståhlbom, F.J.M. van Workum, H. van de Wetering, C. Lundström, S. Smit, A. VilanovaPublished in Computer Graphics Forum by Wiley in 202510.1111/cgf.70147
- 7.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
- 8.Author(s): Yael Tirlet, Matéo Boudet, Emmanuelle Becker, Fabrice Legeai, Olivier DameronPublished in Computational and Structural Biotechnology Journal by Elsevier BV in 2024, page: 4232-424110.1016/j.csbj.2024.11.022
- 9.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: 309-32310.1080/21501203.2024.2358868
- 10.Author(s): Vincenzo Bonnici, Davide ChiccoPublished in BioData Mining by Springer Science and Business Media LLC in 202410.1186/s13040-024-00380-2
- 11.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
- 12.Author(s): Thibault Leroy, Pierre Faux, Benjamin Basso, Sonia Eynard, David Wragg, Alain VignalPublished in Molecular Biology and Evolution by Oxford University Press (OUP) in 202410.1093/molbev/msae249
- 13.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
- 14.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
- 15.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
- 16.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
- 17.Author(s): Sushma Naithani, Cecilia H. Deng, Sunil Kumar Sahu, Pankaj JaiswalPublished in Biomolecules by MDPI AG in 2023, page: 140310.3390/biom13091403
- 18.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
- 19.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
- 1.Author(s): Adam P. Ryan, Sean Bergin, Jillian Scully, Evelyn Zuniga-Soto, Conor Hession, Amelia E. Barber, Emilia Gomez-Molero, Oliver Bader, Florent Morio, Bing Zhai, Kenneth H. Wolfe, Geraldine ButlerPublished by Cold Spring Harbor Laboratory in 202510.1101/2025.04.30.651475
- 2.Author(s): Lakhansing A. Pardeshi, Anne Kupczok, Dick de Ridder, Sandra Smit, Theo A. J. van der LeePublished by Cold Spring Harbor Laboratory in 202510.1101/2025.07.30.667677
- 3.Author(s): Christina Papastolopoulou, Ronald Nieuwenhuis, Sven Warris, Linda V. Bakker, Jan van Haarst, Jan Cordewener, Thamara Hesselink, Hetty van den Broeck, Willem van Dooijeweert, Hans de Jong, Julapark Chunwongse, Sara Diaz Trivino, Elio Schijlen, Dick de Ridder, Sandra Smit, Sander A. PetersPublished by Cold Spring Harbor Laboratory in 202510.1101/2025.06.03.657591
- 4.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 by Cold Spring Harbor Laboratory in 202410.1101/2024.06.20.599299
- 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 by Cold Spring Harbor Laboratory in 202410.1101/2024.10.17.618847
- 6.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
- 7.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
- 8.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
- 9.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
- 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.v2
- 11.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
- 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 202310.36227/techrxiv.21572433
- 13.Author(s): Sushma Naithani, Cecilia H. Deng, Sunil Kumar Sahu, Pankaj JaiswalPublished by MDPI AG in 202310.20944/preprints202308.1641.v1
- 14.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
- 15.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
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