PanTools-pipeline-v4
PA
General purpose Snakemake pipeline for PanTools v4.
Updated 3 months ago
Get started
2138 commits | Last commit ≈ 7 months ago
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.
17
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
Journal articles
6- 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): Sushma Naithani, Cecilia H. Deng, Sunil Kumar Sahu, Pankaj JaiswalPublished in Biomolecules by MDPI AG in 2023, page: 140310.3390/biom13091403
- 3.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
- 4.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
- 5.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
- 6.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
Thesis
2Other
7- 1.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
- 2.Author(s): Sushma Naithani, Cecilia H. Deng, Sunil Kumar Sahu, Pankaj JaiswalPublished in 202310.20944/preprints202308.1641.v1
- 3.Author(s): Astrid van den Brandt, Eef Jonkheer, Dirk-Jan van Workum, Huub van de Wetering, Sandra Smit, Anna VilanovaPublished in 202310.36227/techrxiv.21572433.v2
- 4.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
- 5.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
- 6.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
- 7.Author(s): Astrid van den Brandt, Eef Jonkheer, Dirk-Jan van Workum, Huub van de Wetering, Sandra Smit, Anna VilanovaPublished 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 2 months ago
Finished
Related software
PanVA
PA
Variant Analysis within Pangenomes.
Updated 3 months ago
2 2