Center for Advanced Intelligence Project

🗓 Date & Time

Wednesday, July 2

🕐 13:00 – 14:00 (JST)

📍 Venue

• AIP Open Space (AIP members only)
• Online via Zoom (link will be shared with registered participants)

🎤 Speaker

Giulio Ermanno PIBIRI

Ca’ Foscari University

🔗 GitHub Profile

🧠Organizer

Succinct Information Processing Team in RIKEN-AIP

🧪 Title

The Anatomy of an Order-Preserving k-mer Dictionary

🧬 Abstract

Efficient representation and querying of k-mers is a central challenge in modern bioinformatics, especially in the context of large-scale sequencing data.

In this tutorial, we explore the structure and principles behind order-preserving k-mer dictionaries — succinct data structures designed to store and retrieve k-mers while maintaining their relative ordering.

We begin with a brief overview of de Bruijn graphs and their colored variants, then introduce the motivation and design space for compressed k-mer dictionaries. Emphasis will be placed on the algorithmic techniques that enable order preservation and on how these foundations support advanced tasks such as:

• Repetition-aware compression
• Querying in colored de Bruijn graphs

This session is intended as a gentle but thorough introduction for participants of the main talk.