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Gene prediction with BRAKER3

This session is part of Biodiversity Genomics Academy 2023

Session Leader(s)

Katharina J. Hoff, Institute of Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, Germany.


Welcome to our comprehensive workshop on Structural Genome Annotation with BRAKER3! In this engaging and informative session, we will delve into the intricacies of structural genome annotation, focusing on the utilization of BRAKER3, a powerful tool that leverages RNA-Seq short read data and a large protein database to unravel structures of protein coding genes. Our workshop is designed to equip you with both theoretical knowledge and practical skills, ensuring you leave with a solid grasp of genome annotation principles.

Workshop Contents:

1. Background and Theory:

Our journey begins with a deep dive into the fundamentals of structural genome annotation. You'll gain insights into the underlying concepts of BRAKER3 using RNA-Seq short read data and a large protein database for the annotation of protein=-coding genes.

2. Hands-On Tutorial: Running the BRAKER Container:

Theory seamlessly transitions into practice as we guide you through a hands-on tutorial. You will have the opportunity to roll up your sleeves and start the BRAKER container yourself. Our step-by-step guidance will ensure that you not only understand the theoretical underpinnings but also feel confident in executing the annotation process. By the end of this segment, you'll have a practical understanding of how to harness BRAKER3's potential. (The runtime of the test job will exceed the workshop duration, though.)

3. Exploring Alternative Modes of Running BRAKER:

Diversity is key in the world of genome annotation, and our workshop will explore alternative approaches to employing BRAKER. We will illuminate the process of utilizing BRAKER with RNA-Seq data and navigating the intricacies of working with a large protein database. This segment empowers you to adapt and tailor your annotation strategy to suit specific data sets.

4. Brief Overview of the GALBA Pipeline:

While the spotlight remains on BRAKER3, we'll also briefly introduce you to the GALBA pipeline—a powerful tool for annotating large genomes using protein data from closely related species. This glimpse into an alternative approach expands your toolkit and offers valuable insights into versatile annotation strategies.

5. Interactive Discussion and Q&A:

Throughout the workshop, your engagement is highly encouraged. We recognize that questions and discussions fuel deeper understanding. Our dedicated session for questions and interactive discussion provides you with the opportunity to clarify doubts, share insights, and gain a broader perspective on the intricacies of structural genome annotation.

Prepare to embark on a journey that demystifies structural genome annotation and empowers you with the skills to unravel structures of protein coding genes effectively. By the end of this workshop, you will be well-equipped to tackle genome annotation challenges using BRAKER3 and related tools. Join us and fellow enthusiasts for an engaging and enriching exploration into the world of structural genome annotation.

We look forward to embarking on this learning adventure with you!


Participants are expected to have previous experience using Bash.


You will get the most out of this session if you meet the prerequisites above.

Please also read the description carefully to see if this session is relevant to you.

If you don't meet the prerequisites or change your mind based on the description or are no longer available at the session time, please email tol-training at to cancel your slot so that someone else on the waitlist might attend.

Workshop Materials

All Workshop materials are available at .

The workshop will begin with a talk on which we will explain the key concepts underlying BRAKER and GALBA. Slides can be found at . Subsequently, we will walk through a BRAKER3 tutorial, documented in .