Critical Assessment of Metagenome Interpretation - the second round of challenges

• Published in: bioRxiv
• Main Authors: Meyer, Fernando, Fritz, Adrian, Zhi-Luo Deng, Koslicki, David, Gurevich, Alexey, Robertson, Gary, Zhu, Jie, Jia, Huijue, Kola, Axel, Limasset, Antoine, Kolmogorov, Mikhail, Egan, Rob, Rosen, Gail L, Alexandru Cristian, Zhao, Zhengqiao, Gray, Melissa A, Nissen, Jakob, Zeller, Georg, Paoli, Lucas, Ruscheweyh, Hans-Joachim, Milanese, Alessio, Sunagawa, Shinichi, Alser, Mohammed, Shi, Lizhen, Chen, Bo, Wang, Zhengyang, Wang, Ziye, Huang, Pingqin, You, Ronghui, Sun, Fengzhu, Zhu, Shanfeng, Bertrand, Denis, Tong, Chengxuan, Li, Chenhao, Nagarajan, Niranjan, Renard, Bernhard, Malcher-Miranda, Fabio, Piro, Vitor C, Chikhi, Rayan, Vicedomini, Riccardo, Wang, Zhong, Thomas, Ashleigh, Tremblay, Julien, Dabrowski, Piotr W, Nurk, Sergey, Jorgensen, Tue S, Willassen, Nils P, Klemetsen, Terje, Robertsen, Espen M, Georganas, Evangelos, Yelick, Katherine, C Titus Brown, Lemaitre, Claire, Peterlongo, Pierre, Marchet, Camille, Marijon, Pierre, Irber, Luiz, Brito, Jaqueline J, Lapierre, Nathan, Eskin, Eleazar, Rasmussen, Simon, Sorensen, Soren J, Hansen, Lars H, Trajkovski, Mirko, Kieser, Silas D, Mende, Daniel R, Serghei Mangul, Sarwal, Varuni, Beghini, Francesco, Segata, Nicola, Warren, Andrew, Porter, Jacob S, Rees, Evan R, Kwan, Jason, Clausen, Philip Tlc, Buchmann, Jan, Reinert, Knut, Seiler, Enrico, Korobeynikov, Anton, Antipov, Dmitry, Meleshko, Dmitry, Aydin Buluc, Hofmeyr, Steven, Oliker, Leonid, Goltsman, Eugene, Gherman Uritskiy, Radutoiu, Simona, Gastmeier, Petra, Maechler, Friederike, Khaledi, Ariane, Haussler, Susanne, Smit, Nathiana, Strowig, Till, Garrido-Oter, Ruben, Fantin Mesny, Hacquard, Stephane, Schulze-Lefert, Paul, Bremges, Andreas, Sczyrba, Alexander, Mchardy, Alice C
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 12.07.2021
• Subjects: Genomes; Metagenomics; Plasmids
• DOI: 10.1101/2021.07.12.451567

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the community-driven initiative for the Critical Assessment of Metagenome Interpretation (CAMI). In its second challenge, CAMI engaged the community to assess their methods on realistic and complex metagenomic datasets with long and short reads, created from ~1,700 novel and known microbial genomes, as well as ~600 novel plasmids and viruses. Altogether 5,002 results by 76 program versions were analyzed, representing a 22x increase in results. Substantial improvements were seen in metagenome assembly, some due to using long-read data. The presence of related strains still was challenging for assembly and genome binning, as was assembly quality for the latter. Taxon profilers demonstrated a marked maturation, with taxon profilers and binners excelling at higher bacterial taxonomic ranks, but underperforming for viruses and archaea. Assessment of clinical pathogen detection techniques revealed a need to improve reproducibility. Analysis of program runtimes and memory usage identified highly efficient programs, including some top performers with other metrics. The CAMI II results identify current challenges, but also guide researchers in selecting methods for specific analyses. Competing Interest Statement A.E.D. co-founded Longas Technologies Pty Ltd, a company aimed at development of synthetic long-read sequencing technologies. Footnotes * http://www.cami-challenge.org/