Hi all,

We’re pleased to announce our upcoming course “Assembly and Annotation of Genomes”, taking place 9–13 March. To foster international participation, the course will be held online.

Course website: https://www.physalia-courses.org/courses-workshops/course20/

This comprehensive course introduces biologists and bioinformaticians to the concepts, methods, and practical workflows of de novo genome assembly and annotation, combining theory with hands-on exercises. It is suitable for both beginners and more advanced users, and does not require prior experience with DNA sequencing or Linux.

The course will cover:

• principles and algorithms behind modern genome assembly workflows

• strengths and limitations of sequencing technologies (Illumina, PacBio HiFi/CLR, Oxford Nanopore, Hi-C, optical mapping)

• quality control and evaluation of assemblies (e.g. GenomeScope, Merqury, BUSCO, Pretext)

• consensus improvement, structural error mitigation, and manual curation

• introduction to telomere-to-telomere (T2T) genome assemblies

• genome annotation using Illumina RNA-seq and PacBio Iso-Seq data

Through a mix of lectures and hands-on sessions (using graphical interfaces and basic command line tools), participants will work through key components of a genome assembly and annotation pipeline, with examples inspired by the Vertebrate Genomes Project.

By the end of the course, participants will understand what is required to generate a high-quality, curated, and annotated reference genome, from raw data to downstream-ready resources.

Instructors

• Dr. Giulio Formenti (The Rockefeller University, USA)

• Dr. Guido Gallo (University of Milan, Italy)

Teaching Assistant

• Ying Chen (Vertebrate Genome Lab, The Rockefeller University)

Invited speakers

• Kirsty McCaffrey (The Rockefeller University)

• Aureliano Bombarely (IBMCP, Valencia)

• Marco Sollitto (University of Florence / The Rockefeller University)

• Bonhwang Koo (The Rockefeller University)

Best regards,

Carlo

Carlo Pecoraro, Ph.D

Physalia-courses DIRECTOR

info@physalia-courses.org