Integration of large-scale data for reference genome development in biodiversity

Workshop details
  • Date: Wednesday, September 14th
  • Time: 17:00 to 20:00 CEST
  • Format: Virtual
  • Supported by: Amazon

Using the latest sequencing technologies (long-reads and Hi-C) and advanced bioinformatics methods (including graphs and k-mers) for reference sequence development and data management for global biodiversity and species conservation.


Genomics is a key element for resource management and species protection in biodiversity and conservation research. Advances in genomic sequencing technologies provide opportunities to characterize DNA sequences, RNA sequences and epigenetic patterns of diverse species at a higher resolution. However, processing large-scale sequence data types and genome complexities (for example, large genome sizes, high repeat content, polyploidy) remain challenging. This workshop aims to bring scientific expertise across multiple disciplines – including computer science, bioinformatics, biodiversity, evolutionary biology and genomics – to present strategies and challenges in the generation and evaluation of high-quality reference genomes and in integrative data management for biodiversity. The workshop will focus on: 1) standard data types and assembly methods and pipelines for high-quality reference assemblies, 2) strategies for genome evaluation, and 3) genome annotation, including examples from humans, microbiomes, chicken, salmon and other animal species. Finally, this workshop will facilitate an understanding of the utility of these genomes in large-scale data management in biodiversity management and conservation and for major genome initiatives, including the Earth BioGenome Project, European Reference Genome Atlas, and Africa BioGenome Project.

Target Audience
  • Computer Scientists
  • Geneticists
  • Biodiversity researchers
  • Bioinformaticians
  • Computational and Evolutionary geneticists
5:00 – 5:15 pmWelcome
Shilpa Garg
5:15 – 5:45 pmBiodiversity and bioinformatics
Guojie Zhang
5:45 – 6:15 pmClassified k-mers for genome assembly & analysis
Gene Myers
6:15 – 6:45 pmChromosome-scale haplotype-resolved assembly/pangenomics
Shilpa Garg
6:45 – 7:15 pmCattle pangenomics
Danang Crysnanto
7:15 – 7:30 pm

7:30 – 8:00 pm

Practical session and closing
Shilpa Garg