Fawaz Dabbaghie

gaftools provides utilities for processing graph alignments in GAF format, adapting SAMtools functionalities for pangenome analysis.

Accelign accelerates pairwise sequence alignment using GPUs, achieving significant speedups over existing CPU and GPU implementations for DNA, RNA, and protein sequences.

EpiPAMPAS detects intra-protein epistasis by analyzing multiple sequence alignments and finds interactions with low p-values in simulated and real viral protein data.

The paper introduces extgfa, a low-memory on-disk representation of genome graphs that reduces memory usage for graph operations like BFS by keeping most data on disk.

PanPA generates and aligns panproteome graphs to improve alignment accuracy in prokaryotic genomes by leveraging amino acid similarity over DNA sequence diversity.

BubbleGun efficiently detects bubbles and superbubbles in genome graphs, outperforming existing tools on large datasets.

MetaProFi is a Bloom filter-based tool that stores and queries sequence data, enabling efficient and accurate identification of functionally relevant genetic variants by supporting amino acid and translated nucleotide sequences.