| Literature DB >> 35396482 |
Fernando Meyer1,2, Adrian Fritz1,2,3, Zhi-Luo Deng1,2,4, David Koslicki5, Till Robin Lesker3,6, Alexey Gurevich7, Gary Robertson1,2, Mohammed Alser8, Dmitry Antipov9, Francesco Beghini10, Denis Bertrand11, Jaqueline J Brito12, C Titus Brown13, Jan Buchmann14, Aydin Buluç15,16, Bo Chen15,16, Rayan Chikhi17, Philip T L C Clausen18, Alexandru Cristian19,20, Piotr Wojciech Dabrowski21,22, Aaron E Darling23, Rob Egan24,25, Eleazar Eskin26, Evangelos Georganas27, Eugene Goltsman24,25, Melissa A Gray19,28, Lars Hestbjerg Hansen29, Steven Hofmeyr15,16, Pingqin Huang30, Luiz Irber13, Huijue Jia31,32, Tue Sparholt Jørgensen33,34, Silas D Kieser35,36, Terje Klemetsen37, Axel Kola38, Mikhail Kolmogorov39, Anton Korobeynikov9,40, Jason Kwan41, Nathan LaPierre26, Claire Lemaitre42, Chenhao Li11, Antoine Limasset43, Fabio Malcher-Miranda44, Serghei Mangul12, Vanessa R Marcelino45,46, Camille Marchet43, Pierre Marijon47, Dmitry Meleshko9, Daniel R Mende48, Alessio Milanese49,50, Niranjan Nagarajan51,52, Jakob Nissen53, Sergey Nurk54, Leonid Oliker15,16, Lucas Paoli49, Pierre Peterlongo42, Vitor C Piro44, Jacob S Porter55, Simon Rasmussen56, Evan R Rees41, Knut Reinert57, Bernhard Renard44,58, Espen Mikal Robertsen37, Gail L Rosen19,28,59, Hans-Joachim Ruscheweyh49, Varuni Sarwal26, Nicola Segata10, Enrico Seiler57, Lizhen Shi60, Fengzhu Sun61, Shinichi Sunagawa49, Søren Johannes Sørensen62, Ashleigh Thomas24,63, Chengxuan Tong11, Mirko Trajkovski35,64, Julien Tremblay65, Gherman Uritskiy66, Riccardo Vicedomini17, Zhengyang Wang30, Ziye Wang67, Zhong Wang68,69,70, Andrew Warren55, Nils Peder Willassen37, Katherine Yelick15,16, Ronghui You30, Georg Zeller50, Zhengqiao Zhao19, Shanfeng Zhu71,72, Jie Zhu31,32, Ruben Garrido-Oter73, Petra Gastmeier38, Stephane Hacquard73, Susanne Häußler6, Ariane Khaledi6, Friederike Maechler38, Fantin Mesny73, Simona Radutoiu74, Paul Schulze-Lefert73, Nathiana Smit6, Till Strowig6, Andreas Bremges1,3, Alexander Sczyrba75, Alice Carolyn McHardy76,77,78,79.
Abstract
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.Entities:
Mesh：
Year: 2022 PMID： 35396482 PMCID： PMC9007738 DOI： 10.1038/s41592-022-01431-4
Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547