Critical Assessment of Metagenome Interpretation: the second round of challenges

Meyer F, Fritz A, Deng Z-L, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, et al. (2022)
Nature Methods 19: 429-440.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Autor*in
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 J.
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Abstract / Bemerkung
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.
Erscheinungsjahr
2022
Zeitschriftentitel
Nature Methods
Band
19
Seite(n)
429-440
ISSN
1548-7091
eISSN
1548-7105
Page URI
https://pub.uni-bielefeld.de/record/2962388

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Meyer F, Fritz A, Deng Z-L, et al. Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature Methods. 2022;19:429-440.
Meyer, F., Fritz, A., Deng, Z. - L., Koslicki, D., Lesker, T. R., Gurevich, A., Robertson, G., et al. (2022). Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature Methods, 19, 429-440. https://doi.org/10.1038/s41592-022-01431-4
Meyer, F., Fritz, A., Deng, Z. - L., Koslicki, D., Lesker, T. R., Gurevich, A., Robertson, G., Alser, M., Antipov, D., Beghini, F., et al. (2022). Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature Methods 19, 429-440.
Meyer, F., et al., 2022. Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature Methods, 19, p 429-440.
F. Meyer, et al., “Critical Assessment of Metagenome Interpretation: the second round of challenges”, Nature Methods, vol. 19, 2022, pp. 429-440.
Meyer, F., Fritz, A., Deng, Z.-L., Koslicki, D., Lesker, T.R., Gurevich, A., Robertson, G., Alser, M., Antipov, D., Beghini, F., Bertrand, D., Brito, J.J., Brown, C.T., Buchmann, J., Buluç, A., Chen, B., Chikhi, R., Clausen, P.T.L.C., Cristian, A., Dabrowski, P.W., Darling, A.E., Egan, R., Eskin, E., Georganas, E., Goltsman, E., Gray, M.A., Hansen, L.H., Hofmeyr, S., Huang, P., Irber, L., Jia, H., Jørgensen, T.S., Kieser, S.D., Klemetsen, T., Kola, A., Kolmogorov, M., Korobeynikov, A., Kwan, J., LaPierre, N., Lemaitre, C., Li, C., Limasset, A., Malcher-Miranda, F., Mangul, S., Marcelino, V.R., Marchet, C., Marijon, P., Meleshko, D., Mende, D.R., Milanese, A., Nagarajan, N., Nissen, J., Nurk, S., Oliker, L., Paoli, L., Peterlongo, P., Piro, V.C., Porter, J.S., Rasmussen, S., Rees, E.R., Reinert, K., Renard, B., Robertsen, E.M., Rosen, G.L., Ruscheweyh, H.-J., Sarwal, V., Segata, N., Seiler, E., Shi, L., Sun, F., Sunagawa, S., Sørensen, S.J., Thomas, A., Tong, C., Trajkovski, M., Tremblay, J., Uritskiy, G., Vicedomini, R., Wang, Z., Wang, Z., Wang, Z., Warren, A., Willassen, N.P., Yelick, K., You, R., Zeller, G., Zhao, Z., Zhu, S., Zhu, J., Garrido-Oter, R., Gastmeier, P., Hacquard, S., Häußler, S., Khaledi, A., Maechler, F., Mesny, F., Radutoiu, S., Schulze-Lefert, P., Smit, N., Strowig, T., Bremges, A., Sczyrba, A., McHardy, A.C.: Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature Methods. 19, 429-440 (2022).
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 J., Brown, C. Titus, Buchmann, Jan, Buluç, Aydin, Chen, Bo, Chikhi, Rayan, Clausen, Philip T. L. C., Cristian, Alexandru, Dabrowski, 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 D., Klemetsen, Terje, Kola, Axel, Kolmogorov, Mikhail, Korobeynikov, Anton, Kwan, Jason, LaPierre, Nathan, Lemaitre, Claire, Li, Chenhao, Limasset, Antoine, Malcher-Miranda, Fabio, Mangul, Serghei, Marcelino, Vanessa R., Marchet, Camille, Marijon, Pierre, Meleshko, Dmitry, Mende, Daniel R., Milanese, Alessio, Nagarajan, Niranjan, Nissen, Jakob, Nurk, Sergey, Oliker, Leonid, Paoli, Lucas, Peterlongo, Pierre, Piro, Vitor C., Porter, Jacob S., Rasmussen, Simon, Rees, Evan R., Reinert, Knut, Renard, Bernhard, Robertsen, Espen Mikal, Rosen, Gail L., Ruscheweyh, Hans-Joachim, Sarwal, Varuni, Segata, Nicola, Seiler, Enrico, Shi, Lizhen, Sun, Fengzhu, Sunagawa, Shinichi, Sørensen, Søren Johannes, 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, Ruben, Gastmeier, Petra, Hacquard, Stephane, Häußler, Susanne, Khaledi, Ariane, Maechler, Friederike, Mesny, Fantin, Radutoiu, Simona, Schulze-Lefert, Paul, Smit, Nathiana, Strowig, Till, Bremges, Andreas, Sczyrba, Alexander, and McHardy, Alice Carolyn. “Critical Assessment of Metagenome Interpretation: the second round of challenges”. Nature Methods 19 (2022): 429-440.
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PMID: 35396482
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Preprint: 10.1101/2021.07.12.451567

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