ASVA-CGR
Algorithms for Structural Variation Analysis in Challenging Genomic Regions
Funded under the “HORIZON.4.1 - Widening participation and spreading excellence” programme.
Grant agreement ID: 101180581
Funding scheme: HORIZON TMA MSCA Postdoctoral Fellowships - European Fellowships.
https://doi.org/10.3030/101180581
Outcomes
The project outcomes can be summarized in two categories:
- pangenomics
- genetic variations
Pangenomics
Genetic Variations
Publications
-
A. Petescia, L. Denti, A. Gafurov, V. Hodorova, J. Nosek, B. Brejova, T. Vinar
Alignment-free Detection of Differences Between Sequencing Data Sets
iScience (2025) -
D. Cozzi, B. Riccardi, L. Denti, S. Ciccolella, K. Sadakane, P. Bonizzoni
Pangenome Graph Indexing via the Multidollar-BWT
SEA Proceedings (2025) -
L. Denti, Y. Shibuya
Weighted de novo clustering of third-generation transcriptomic datasets
ITAT Proceedings (2025) -
L. Denti, P. Bonizzoni, B. Brejova, R. Chikhi, T. Krannich, T. Vinar, F. Hormozdiari
Pangenome graph augmentation from unassembled long reads
bioRxiv (2025) -
L. Denti, T. Krannich, T. Vinar, R. Chikhi, P. Bonizzoni, B. Brejova, F. Hormozdiari
Anyone can be the best: Impact of diverse methodologies on the evaluation of structural variant callers
bioRxiv (2025) -
S. Ciccolella, D. Cozzi, G. Della Vedova, S. Kuria, P. Bonizzoni, L. Denti
Differential quantification of alternative splicing events on spliced pangenome graphs
PLOS Computational Biology (2024)
Software
- palss, a tool for augmenting pangenome graph from unassembled long reads (WIP)
- svbench-fw, a modular and extensible framework to evaluate SV callers
- pantas, a tool for quantifying AS events from spliced pangenome graphs
- kdiff, a tool for the alignment-free detection of differences between sequencing data sets
- SolidClust, a method for the de novo clustering of third-generation transcriptomic datasets
- GIndex, a multidollar-BWT based graph index
Slides and Posters
Invited talks:
-
Future impact of ALPACA / Open problems on pangenomes
Final workshop of the ALPACA ITN Project (St. Malo, France - December 9-11, 2024) -
Pangenome graph augmentation from unassembled long reads
Pangenome Bio Hacking 2025 Workshop (online - January 22-24, 2025) -
Foundations of Sequence Bioinformatics
The Human Pangenome Project - For an inclusive genomics (Milano, Italy - July 9, 2026)
Talks:
- Pangenome graph augmentation from unassembled long reads
RECOMBSEQ2025. Seoul, South Korea
ITAT25. Telgart, Slovakia
Posters: