Paper
Document
Download
Flag content
82

Critical Assessment of Metagenome Interpretation - the second round of challenges

Authors
Fernando Meyer,Adrian Fritz
Zhi-Luo Deng,David Koslicki,Alexey Gurevich,Gary Robertson,Mohammed Alser,Dmitry Antipov,Francesco Beghini,Denis Bertrand,Jaqueline Brito,Christopher Brown,Jan Buchmann,Aydın Buluç,B. Chen,Rayan Chikhi,Philip Clausen,Alexandru Cristian,Piotr Dabrowski,Aaron Darling,Rob Egan,Eleazar Eskin,Evangelos Georganas,Eugene Goltsman,Melissa Gray,Lars Hansen,Steven Hofmeyr,Pei Huang,Luiz Irber,Huijue Jia,Tue Jørgensen,Silas Kieser,Terje Klemetsen,Axel Kola,Mikhail Kolmogorov,Anton Korobeynikov,Jason Kwan,Nathan LaPierre,Claire Lemaitre,C. Li,Antoine Limasset,Fábio Miranda,Serghei Mangul,Vanesa Marcelino,Camille Marchet,Pierre Marijon,Dmitry Meleshko,Daniel Mende,Alessio Milanese,Niranjan Nagarajan,Jakob Nissen,Sergey Nurk,Leonid Oliker,Lucas Paoli,Pierre Peterlongo,Vitor Piro,Jacob Porter,Simon Rasmussen,Evan Rees,Knut Reinert,Bernhard Renard,Espen Robertsen,Gail Rosen,Hans‐Joachim Ruscheweyh,Varuni Sarwal,Nicola Segata,Enrico Seiler,Lizhen Shi,Fengzhu Sun,Shinichi Sunagawa,Søren Sørensen,Ashleigh Thomas,Chengxuan Tong,Mirko Trajkovski,Julien Tremblay,Gherman Uritskiy,Riccardo Vicedomini,Zi. Wang,Zhe Wang,Zho. Wang,Andrew Warren,Nils Willassen,Katherine Yelick,Ronghui You,Georg Zeller,Zhengqiao Zhao,Shanfeng Zhu,Jun Zhu,Ruben Garrido‐Oter,Petra Gastmeier,Stéphane Hacquard,Susanne Häußler,Ariane Khaledi,Friederike Maechler,Fantin Mesny,Simona Radutoiu,Paul Schulze‐Lefert,Nathiana Smit,Till Strowig,Andreas Bremges,Alexander Sczyrba,Francesca Filippis,Cristian Gallo,Pei‐Qiang Huang,China Li,Vanessa Marcelino,Kenneth Jansen,Catherine Tong,Zhong Wang
+107 authors
,Alice McHardy
Published
Jul 12, 2021
Show more
Save
TipTip
Document
Download
Flag content
82
TipTip
Save
Document
Download
Flag content

Abstract

Abstract 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.

Paper PDF

This paper's license is marked as closed access or non-commercial and cannot be viewed on ResearchHub. Visit the paper's external site.