Seminars

Speaker: Bastien Degardins

Room: Amphi Atrium (RdC Bâtiment ESPRIT)

Title: Visualization and queries for biology in de Bruijn Graphs using relational databases.

Abstract:

Since the emergence of modern sequencers, sequence bioinformatics has become
crucial for processing sequencing data, essential in medicine, biology,
archaeology, and beyond. However, the growing data volumes require software
adaptations to meet these new challenges, despite significant hardware
advancements. Vizitig is a genomic and transcriptomic data visualization
software based on De Bruijn graphs, offering an intuitive query system without
needing to load indexes into RAM, allowing direct work on disk. By leveraging
relational databases, which are highly optimized and backed by decades of
research, Vizitig opens new avenues for research.It relies on NetworkDisk, a
Python package that manages graphs in a relational database, simplifying
software engineering. With a domain-specific language (DSL), Vizitig enables
intuitive queries and easy manipulation of graph metadata, even for
non-technical users. For experts, its compatibility with NetworkX provides
additional possibilities in terms of graph manipulation.