Adam Gudyś

This paper organizes a community challenge to develop automated virus taxonomy classification tools and evaluates their performance on a combined dataset of expert-curated and metagenomic sequences.

FAMSA2 provides high-accuracy multiple sequence alignments for large-scale protein datasets with significantly improved speed.

The paper presents an nf-core framework for comparing multiple sequence aligners, aiming to streamline deployment and evaluation of MSA tools in HPC environments.

Vclust clusters viral genomes efficiently and accurately using Lempel-Ziv parsing for average nucleotide identity, outperforming existing tools.

ProteStAr compresses protein structure files efficiently, offering better compression ratios than existing tools while maintaining reconstruction accuracy.

The paper introduces SPLASH and compactors to efficiently discover microbial genetic elements and perform strain typing without reference genomes.

CoLoRd compresses third-generation sequencing data by an order of magnitude without affecting downstream analysis accuracy.

PHIST predicts prokaryotic hosts of viruses from their genomic sequences, improving accuracy and speed over existing methods.

Whisper 2 improves indel variant calling quality while maintaining fast runtime compared to existing short-read-mapping tools.

Whisper improves sequencing data mapping by sorting reads and using suffix arrays, achieving faster performance with comparable accuracy to Bowtie2 and BWA-MEM.

Kmer-db estimates evolutionary distances between pathogens using k-mers, achieving 44x faster performance than Mash on a modern workstation.