Dirk-Jan M. van Workum

Dirk-Jan M. van Workum

PhD candidate in the Bioinformatics Group (WUR); member of the LettuceKnow consortium

Software

PanTools Permalink

Bioinformatics, Wageningen University & Research

For my PhD (2020-2025) I have developed several major features for PanTools as well as general code improvements. I was involved in designing new features for versions 3 and 4, and I have been one of the maintainers of version 4. Some of the major features I have worked on include: (1) Implementation of integrating PAV and VCF data into a pangenome graph for gene analysis. (2) Implementation of a region of interest analysis in pangenomic context. (3) Update of PanTools to Java 21 and neo4j 5.

MoGAAAP Permalink

Bioinformatics, Wageningen University & Research

During my PhD (2020-2025) I have developed the workflow MoGAAAP (Modular Genome Assembly, Annotation and Quality Assessment Pipeline), written in Snakemake. This pipeline is designed to automate the assembly, annotation and QA of sets of genomes with the aim of constructing population-level pangenomes. It is modular, so that it can also be used for e.g. the annotation and QA of an already existing assembly.