LRG

This repository contains the material for the Long Read Genomics courses.

• First course was given at at CZU in Prague in early November 2025.
• Second course will take place at University of Thessaly

Topics for lectures at University of Thessaly

• Sequencing technologies
• ONT-based plant genomics workflow
• Structural annotation
• Functional annotation
• Data submission

Topics for lectures in Prague

• (1) Sequencing Technologies
• (2) Plant Genome Sequencing with ONT
• (3) Generating a Structural & Functional Annotation
• (4) Read Mapping and Variant Calling
• (5) Submitting Sequencing Data and Reusing Public Data

Questions or interested in a meeting?

Please send any questions you might have via email to Boas Pucker.

References

• Pucker B, Irisarri I, de Vries J and Xu B (2022). Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions. Quantitative Plant Biology, 3, E5. doi: 10.1017/qpb.2021.18.
• Natarajan et al., 2026. Functional Annotation – How to Tackle the Bottleneck in Plant Genomics. Zenodo. doi: 10.5281/zenodo.18761275.
• de Oliveira, J. A. V. S.; Choudhary, N.; Meckoni, S. N.; Nowak, M. S.; Hagedorn, M.; Pucker, B. (2026). Cookbook for Plant Genome Sequences. BMC Genomics (2026). doi: 10.1186/s12864-026-12623-z.