Educators:
Prof. Dr. Boas Pucker, Katharina Wolff, Nancy Choudhary, Shakunthala Natarajan, Samuel Nestor Meckoni, Julie A. V. S. De Oliveira (Associated Partner)

Date:
08.12.2025-10.12.2025

Location:
Kirschallee 1, 53115 Bonn, Germany

Contents:
Unlock the secrets of plant genomes with this intensive, hands-on course in "Plant Genome Sequence Assembly and Annotation". Designed for doctoral students and postdoctoral researcher in genomics and bioinformatics, this course offers practical training in processing and assembling Oxford Nanopore Technologies (ONT) long-read sequencing data. Participants will learn to perform quality control, assemble high-quality plant genome sequences using tools like HERRO, Shasta, and NextDenovo2, and carry out structural genome sequence annotation with HISAT2/STAR, GeMoMa, and BUSCO. The course emphasizes real-world applications, providing participants with the skills to interpret, validate, and refine genome assemblies and gene models specific to plant systems. Whether you are starting your first genome project or looking to enhance your bioinformatics toolkit, this course will give you the expertise to tackle complex plant genomic data with confidence.

Learning goals:
How to get from ONT long reads to a genome sequence with corresponding gene models

Prerequisites:
Basic experience with command line

Keywords:
genome sequence, assembly, long reads, gene models, plant genomics

Tools:
HERRO, Shasta, NextDenovo2, HISAT2/STAR, BUSCO, GeMoMa