SuRankCo: supervised ranking of contigs in de novo assemblies. - Mathias Kuhring; Piotr Wojtek Dabrowski; Vitor Piro; Andreas Nitsche; Bernhard Y. Renard (BMC Bioinform., 2015)

DUDes: a top-down taxonomic profiler for metagenomics. - Vitor Piro; Martin S. Lindner; Bernhard Y. Renard (Bioinform., 2016)

DREAM-Yara: an exact read mapper for very large databases with short update time. - Temesgen Hailemariam Dadi; Enrico Siragusa; Vitor Piro; Andreas Andrusch; Enrico Seiler; Bernhard Y. Renard; Knut Reinert (Bioinform., 2018)

Reference and taxonomy based methods for classification and abundance estimation of organisms in metagenomic samples - Vitor Piro (2018)

ganon: precise metagenomics classification against large and up-to-date sets of reference sequences. - Vitor Piro; Temesgen Hailemariam Dadi; Enrico Seiler; Knut Reinert; Bernhard Y. Renard (Bioinform., 2020)

Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2. - Fábio Malcher Miranda; Vasco Ariston de Carvalho Azevedo; Rommel Thiago Juca Ramos; Bernhard Y. Renard; Vitor Piro (BMC Bioinform., 2024)