Vitor C. Piro

This paper introduces a dynamic and updatable sequence-search index called Dynamic HIBF, which efficiently handles large-scale data updates and outperforms existing methods in speed.

ganon2 improves metagenomics analysis by providing faster, more accurate taxonomic binning and profiling with smaller reference indices.

HiTaC is a hierarchical machine learning model for fungal ITS sequence classification that outperforms existing methods on noisy data.

GRIMER detects contamination in microbiome studies by integrating multiple evidence sources and generating an interactive dashboard for data exploration.

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

Ganon improves metagenomics classification by efficiently indexing and updating large reference sequence sets, increasing read classification and species identification compared to existing tools.

DREAM-Yara provides an efficient read mapper for large reference databases, reducing index construction time and enabling faster updates.

Bioconda provides a sustainable, comprehensive distribution of bioinformatics software using Conda for reproducible analysis across platforms.

The paper benchmarks computational metagenomics software using complex datasets, showing strengths and limitations in assembly, binning, and taxonomic profiling.

MetaMeta integrates multiple metagenome analysis tools to improve taxonomic profiling by combining results from different methods.