Critical Assessment of Metagenome Interpretation: the second round of challenges

Meyer, Fernando; Fritz, Adrian; Deng, Zhi-Luo; Koslicki, David; Lesker, Till Robin; Gurevich, Alexey; Robertson, Gary; Alser, Mohammed; Antipov, Dmitry; Beghini, Francesco; Bertrand, Denis; Brito, Jaqueline; Brown, C. Titus; Buchmann, Jan P.; Buluç, Aydın; Chen, Bo; Chikhi, Rayan; Clausen, Philip T. L. C.; Cristian, Alexandru; Dąbrowski, Piotr Wojciech; Darling, Aaron E.; Egan, Rob; Eskin, Eleazar; Georganas, Evangelos; Goltsman, Eugene; Gray, Melissa A.; Hansen, Lars Hestbjerg; Hofmeyr, Steven; Huang, Pingqin; Irber, Luiz; Jia, Huijue; Jørgensen, Tue Sparholt; Kieser, Silas; Klemetsen, Terje; Kola, Axel; Kolmogorov, Mikhail; Korobeynikov, Anton; Kwan, Jason C.; LaPierre, Nathan; Lemaitre, Claire; Li, Chenhao; Limasset, Antoine; Miranda, Fábio Malcher; Mangul, Serghei; Marcelino, Vanessa R.; Marchet, Camille; Marijon, Pierre; Meleshko, Dmitry; Mende, Daniel R.; Milanese, Alessio; Nagarajan, Niranjan; Nissen, Jakob Nybo; Nurk, Sergey; Oliker, Leonid; Paoli, Lucas; Peterlongo, Pierre; Piro, Vitor C.; Porter, Jacob S.; Rasmussen, Simon; Rees, Evan; Reinert, Knut; Renard, Bernhard Y.; Robertsen, Espen Mikal; Rosen, Gail; Ruscheweyh, Hans‐Joachim; Sarwal, Varuni; Segata, Nicola; Seiler, Enrico; Shi, Lizhen; Sun, Fengzhu; Sunagawa, Shinichi; Sørensen, Søren J.; Thomas, Ashleigh; Tong, Chengxuan; Trajkovski, Mirko; Tremblay, Julien; Uritskiy, Gherman; Vicedomini, Riccardo; Wang, Zhengyang; Wang, Ziye; Wang, Zhong; Warren, Andrew; Willassen, Nils Peder; Yelick, Katherine; You, Ronghui; Zeller, Georg; Zhao, Zhengqiao; Zhu, Shanfeng; Zhu, Jie; Garrido‐Oter, Rubén; Gastmeier, Petra; Hacquard, Stéphane; Häußler, Susanne; Khaledi, Ariane; Maechler, Friederike; Mesny, Fantin; Radutoiu, Simona; Schulze‐Lefert, Paul; Smit, Nathiana; Strowig, Till; Bremges, Andreas; Sczyrba, Alexander; McHardy, Alice C.

doi:10.1038/s41592-022-01431-4

articleNature MethodsApr 1, 2022HYBRID OA

Critical Assessment of Metagenome Interpretation: the second round of challenges

FMFernando Meyer AFAdrian Fritz ZDZhi-Luo Deng DKDavid Koslicki TRTill Robin Lesker

Helmholtz Centre for Infection Research · Technische Universität Braunschweig · +58 more institutions

PubMed

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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…

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390

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Percentile: 100%
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Topics & keywords

Topics

Keywords

Metagenomics
Computational biology
Interpretation (philosophy)
Biology
Computer science
Genetics
Gene

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