Bioconda: sustainable and comprehensive software distribution for the life sciences B Grüning, R Dale, A Sjödin, BA Chapman, J Rowe, CH Tomkins-Tinch, ... Nature methods 15 (7), 475-476, 2018 | 789 | 2018 |
Critical assessment of metagenome interpretation—a benchmark of metagenomics software A Sczyrba, P Hofmann, P Belmann, D Koslicki, S Janssen, J Dröge, ... Nature methods 14 (11), 1063-1071, 2017 | 727 | 2017 |
Critical assessment of metagenome interpretation: the second round of challenges F Meyer, A Fritz, ZL Deng, D Koslicki, TR Lesker, A Gurevich, G Robertson, ... Nature methods 19 (4), 429-440, 2022 | 182 | 2022 |
FGAP: an automated gap closing tool VC Piro, H Faoro, VA Weiss, MBR Steffens, FO Pedrosa, EM Souza, ... BMC research notes 7, 1-5, 2014 | 78 | 2014 |
DUDes: a top-down taxonomic profiler for metagenomics VC Piro, MS Lindner, BY Renard Bioinformatics 32 (15), 2272-2280, 2016 | 51 | 2016 |
MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling VC Piro, M Matschkowski, BY Renard Microbiome 5, 1-11, 2017 | 47 | 2017 |
DREAM-Yara: an exact read mapper for very large databases with short update time TH Dadi, E Siragusa, VC Piro, A Andrusch, E Seiler, BY Renard, K Reinert Bioinformatics 34 (17), i766-i772, 2018 | 40 | 2018 |
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences VC Piro, TH Dadi, E Seiler, K Reinert, BY Renard Bioinformatics 36 (Supplement_1), i12-i20, 2020 | 36* | 2020 |
SuRankCo: supervised ranking of contigs in de novo assemblies M Kuhring, PW Dabrowski, VC Piro, A Nitsche, BY Renard BMC bioinformatics 16, 1-7, 2015 | 13 | 2015 |
gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms M Munoz-Benavent, F Hartkopf, T Van Den Bossche, VC Piro, ... NAR genomics and bioinformatics 2 (3), lqaa058, 2020 | 11 | 2020 |
Draft Genome Sequence of Herbaspirillum huttiense subsp. putei IAM 15032, a Strain Isolated from Well Water V de Souza, VC Piro, H Faoro, MZ Tadra-Sfeir, VK Chicora, D Guizelini, ... Genome announcements 1 (1), 10.1128/genomea. 00252-12, 2013 | 9 | 2013 |
Contamination detection and microbiome exploration with GRIMER VC Piro, BY Renard GigaScience 12, giad017, 2023 | 7 | 2023 |
Benchmark data sets, software results and reference data for the first CAMI challenge A Sczyrba, P Hofman, P Belmann, D Koslicki, S Janssen, J Dröge, ... GigaScience Database, 2017 | 4 | 2017 |
ganon2: up-to-date and scalable metagenomics analysis VC Piro, K Reinert bioRxiv, 2023.12. 07.570547, 2023 | | 2023 |
HiTaC: Hierarchical Taxonomic Classification of Fungal ITS Sequences FM Miranda, VAC Azevedo, BY Renard, VC Piro, RTJ Ramos bioRxiv, 2020.04. 24.014852, 2020 | | 2020 |
Reference and taxonomy based methods for classification and abundance estimation of organisms in metagenomic samples VC Piro | | 2018 |
Desenvolvimento da ferramenta para finalização de montagens de genomas in silico-FGAP VC Piro | | 2014 |
JFINISHER finalizador de montagem e editor de sequências biológicas VC Piro | | |