DSB 2023

These are notes for DSB 2023.

Day 1, Tuesday

Practical data structures for longest common extensions, Alexander Herlez

notes go here

Pan-genome de Bruijn graph using the bidirectional FM-index, Lore Depuydt

Indexing large metagenomics projects with abundances, Pierre Peterlongo

µ-PBWT: Enabling the Storage and Use of UK Biobank Data on a Commodity Laptop, Davide Cozzi

Genome-on-Diet: Taming Large-Scale Genomic Analyses via Sparsified Genomics, Mohammed Alser

Spectrum preserving tilings enable sparse and modular reference indexing, Giulio Ermanno Pibiri

Towards a lower-memory chunked graph data structure inspired by Minecraft, Fawaz Dabbaghie

Optimal Worst-Case Design of Gapped k-mer Masks, Sven Rahmann

Locality-Preserving Hashing of k-mers, Yoshihiro Shibuya

Space-efficient k-mer counting using an implicit sequence representation, Miika Leinonen

VeChat: correcting errors in long reads using variation graphs, Alexander Schönhuth

Fixing homopolymer errors in HiFi reads using dictionary compression, Diego Diaz-Dominguez

Orthanq: orthogonal evidence based haplotype quantification, Hamdiye Uzuner

Day 2, Wednesday

Random Wheeler graphs, Riccardo Maso

The Graph Wheelerization Problem, Davide Tonetto

Sorting Wheeler NFA’s using relational partition refinement, Bojana Kodric

Prefix-sorting strings on deterministic finite automata, Sung-Hwan Kim

MARIA: Multiple alignment r-index with aggregation, Adrián Goga

Approximate pattern matching using search schemes and in-text verification, Luca Renders

Chaining of maximal exact matches in graphs, Nicola Rizzo

RecGraph: recombination-aware alignment of sequences to variation graphs, Jorge Avila Cartes

Exact string alignments to (E)D-texts, Nadia Pisanti

Periodicity of degenerate strings, Pengfei Wang

Deriving polygenic risk score using non-negative matrix factorization, Vu Lam Dang

Identifying antimicrobial resistance gene transfer between plasmids, Marco Teixeira