25–29 May 2026

Hellenic Centre for Marine Research (HCMR)
Heraklion Crete, Greece

Marine genomics is rapidly transforming our understanding of marine biodiversity, adaptation, and evolution. This course provides participants with both theoretical foundations and practical skills to analyse genomic datasets in a marine context. Over five days, participants will be introduced to the core concepts of marine and population genomics, learn how to process and assess genomic resources, and apply integrative approaches that link genetic variation to environmental data (seascape genomics).
The course combines lectures, discussions, and extensive hands-on sessions, using real marine datasets. By the end of the course, participants will be able to design and conduct basic analyses in marine genomics, critically evaluate genomic resources, and interpret results within the context of ecological and evolutionary research.

This course is designed for graduate students, postdocs, or researchers with little to no prior experience in marine and population genomics. The primary objective is to learn the field through a hands-on, learning-by-doing approach.
Participants should have a basic understanding of genetics/genomics and evolutionary biology, as well as prior experience with a programming language. Familiarity with UNIX-based command line tools and R is required.
To ensure you can follow the course effectively, we recommend that participants without prior experience in R complete this R tutorial  and those without knowledge of the UNIX command line complete this UNIX tutorial before attending.

By completing this course, participants will gain theoretical and practical experience in:

- Assessing the quality of genome assemblies and reference resources (e.g., BUSCO, QUAST, annotation checks).
- Processing sequencing data (quality control, trimming, mapping, variant calling, filtering).
- Extracting genomic metrics (genetic diversity, allele frequencies, population structure, demographic inference).
- Applying population genomics approaches with real marine datasets.
- Integrating genomic and environmental data for seascape genomics analyses.
- Running and interpreting association analyses linking genetic variation with environmental parameters.
- Critically evaluating results and discussing applications of marine genomics in ecology, conservation, and fisheries.

Daily sessions,  09:00-16:00 Eastern European Time

Day 1  Introduction to Marine Genomics & Genome Resources
Course overview and introductions
Introduction to marine genomics: opportunities and challenges
Sequencing technologies and data analysis
Hands-on: Exploring genome assemblies
Download and assess genomes (BUSCO, QUAST, etc.)
Check genome annotation (GFF files)
Evaluate reference genome quality (size, masked/unmasked, completeness, usability considerations)

Day 2 – Sequencing Data Processing and Variant Calling
Read alignment and genome references
Hands-on: Quality control, trimming, and mapping of NGS data
Variant calling pipelines (SNPs/indels)
Filtering and preparation of datasets for downstream analyses
Practical exercises

Day 3 – Population Genomics Approaches
Introduction to population genomics concepts
Genetic diversity, population structure, and demographic inference
Hands-on: Population genomics analyses with marine datasets

Day 4 – Seascape Genomics: Linking Genomics with Environmental Data
Environmental data collection and parameters for seascape genomics
Data integration: preparing environmental datasets for analysis
Case studies in seascape genomics
Hands-on: Working with environmental datasets

Day 5 – Integrative Analyses: Environment–Genomics Associations
Statistical approaches to link genomic variation with environmental parameters
Seascape genomics models and tools
Hands-on: Running association analyses and interpreting results
Final discussion and wrap-up