Scaling up pangenomics for plant breeding

Delivering a pangenome approach that drastically improves the analytical power on plant data

To capture and capitalize on genetic variation, the field of comparative genomics is switching from a reference-based approach to pangenomic approaches. The main aim of this project was to improve the scalability of our pangenomics software, called PanTools, for large-scale applications in plant sciences and biotechnology. We envisioned improvements in the data representation, in the construction and annotation algorithms, and in the use of novel technologies like Apache Spark. In addition, we aimed to improve our development efforts and make the code base more sustainable by reorganizing/refactoring, writing proper unit tests, and improving the documentation.

Participating organisations

SURF
Life Sciences
Life Sciences
Netherlands eScience Center
Wageningen University & Research

Output

Team

SS
Sandra Smit
Principal investigator
Wageningen University and Research
Thijs van Lankveld
Thijs van Lankveld
Lead RSE
Netherlands eScience Center
NA
Nauman Ahmed

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Related software

PanTools

P

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.

Updated 2 months ago
11 3

PanTools-pipeline-v4

PA

General purpose Snakemake pipeline for PanTools v4.

Updated 2 months ago

PanVA

PA

Variant Analysis within Pangenomes.

Updated 2 months ago
1 2