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dc.contributor.authorMeyer, Fernando
dc.contributor.authorFritz, Adrian
dc.contributor.authorDeng, Zhi-Luo
dc.contributor.authorKoslicki, David
dc.contributor.authorLesker, Till Robin
dc.contributor.authorGurevich, Alexey
dc.contributor.authorRobertson, Gary
dc.contributor.authorAlser, Mohammed
dc.contributor.authorAntipov, Dmitry
dc.contributor.authorBeghini, Francesco
dc.contributor.authorBertrand, Denis
dc.contributor.authorBrito, Jaqueline J.
dc.contributor.authorBrown, C. Titus
dc.contributor.authorBuchmann, Jan
dc.contributor.authorBuluç, Aydin
dc.contributor.authorChen, Bo
dc.contributor.authorChikhi, Rayan
dc.contributor.authorClausen, Philip T. L. C.
dc.contributor.authorCristian, Alexandru
dc.contributor.authorDabrowski, Piotr Wojciech
dc.contributor.authorDarling, Aaron E.
dc.contributor.authorEgan, Rob
dc.contributor.authorEskin, Eleazar
dc.contributor.authorGeorganas, Evangelos
dc.contributor.authorGoltsman, Eugene
dc.contributor.authorGray, Melissa A.
dc.contributor.authorHansen, Lars Hestbjerg
dc.contributor.authorHofmeyr, Steven
dc.contributor.authorHuang, Pingqin
dc.contributor.authorIrber, Luiz
dc.contributor.authorJia, Huijue
dc.contributor.authorJørgensen, Tue Sparholt
dc.contributor.authorKieser, Silas D.
dc.contributor.authorKlemetsen, Terje
dc.contributor.authorKola, Axel
dc.contributor.authorKolmogorov, Mikhail
dc.contributor.authorKorobeynikov, Anton
dc.contributor.authorKwan, Jason
dc.contributor.authorLaPierre, Nathan
dc.contributor.authorLemaitre, Claire
dc.contributor.authorLi, Chenhao
dc.contributor.authorLimasset, Antoine
dc.contributor.authorMalcher-Miranda, Fabio
dc.contributor.authorMangul, Serghei
dc.contributor.authorMarcelino, Vanessa R.
dc.contributor.authorMarchet, Camille
dc.contributor.authorMarijon, Pierre
dc.contributor.authorMeleshko, Dmitry
dc.contributor.authorMende, Daniel R.
dc.contributor.authorMilanese, Alessio
dc.contributor.authorNagarajan, Niranjan
dc.contributor.authorNissen, Jakob
dc.contributor.authorNurk, Sergey
dc.contributor.authorOliker, Leonid
dc.contributor.authorPaoli, Lucas
dc.contributor.authorPeterlongo, Pierre
dc.contributor.authorPiro, Vitor C.
dc.contributor.authorPorter, Jacob S.
dc.contributor.authorRasmussen, Simon
dc.contributor.authorRees, Evan R.
dc.contributor.authorReinert, Knut
dc.contributor.authorRenard, Bernhard
dc.contributor.authorRobertsen, Espen Mikal
dc.contributor.authorRosen, Gail L.
dc.contributor.authorRuscheweyh, Hans-Joachim
dc.contributor.authorSarwal, Varuni
dc.contributor.authorSegata, Nicola
dc.contributor.authorSeiler, Enrico
dc.contributor.authorShi, Lizhen
dc.contributor.authorSun, Fengzhu
dc.contributor.authorSunagawa, Shinichi
dc.contributor.authorSørensen, Søren Johannes
dc.contributor.authorThomas, Ashleigh
dc.contributor.authorTong, Chengxuan
dc.contributor.authorTrajkovski, Mirko
dc.contributor.authorTremblay, Julien
dc.contributor.authorUritskiy, Gherman
dc.contributor.authorVicedomini, Riccardo
dc.contributor.authorWang, Zhengyang
dc.contributor.authorWang, Ziye
dc.contributor.authorWang, Zhong
dc.contributor.authorWarren, Andrew
dc.contributor.authorWillassen, Nils Peder
dc.contributor.authorYelick, Katherine
dc.contributor.authorYou, Ronghui
dc.contributor.authorZeller, Georg
dc.contributor.authorZhao, Zhengqiao
dc.contributor.authorZhu, Shanfeng
dc.contributor.authorZhu, Jie
dc.contributor.authorGarrido-Oter, Ruben
dc.contributor.authorGastmeier, Petra
dc.contributor.authorHacquard, Stephane
dc.contributor.authorHäußler, Susanne
dc.contributor.authorKhaledi, Ariane
dc.contributor.authorMaechler, Friederike
dc.contributor.authorMesny, Fantin
dc.contributor.authorRadutoiu, Simona
dc.contributor.authorSchulze-Lefert, Paul
dc.contributor.authorSmit, Nathiana
dc.contributor.authorStrowig, Till
dc.contributor.authorBremges, Andreas
dc.contributor.authorSczyrba, Alexander
dc.contributor.authorMcHardy, Alice Carolyn
dc.date.accessioned2022-08-16T07:20:19Z
dc.date.available2022-08-16T07:20:19Z
dc.date.issued2022-04-08
dc.description.abstractEvaluating 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.en_US
dc.identifier.citationMeyer, Fritz, Deng, Koslicki, Lesker, Gurevich, Robertson, Alser, Antipov, Beghini, Bertrand, Brito, Brown, Buchmann, Buluç, Chen, Chikhi, Clausen, Cristian, Dabrowski, Darling, Egan, Eskin, Georganas, Goltsman, Gray, Hansen, Hofmeyr, Huang, Irber, Jia, Jørgensen, Kieser, Klemetsen, Kola, Kolmogorov, Korobeynikov, Kwan, LaPierre, Lemaitre, Li, Limasset, Malcher-Miranda, Mangul, Marcelino, Marchet, Marijon, Meleshko, Mende, Milanese, Nagarajan, Nissen, Nurk, Oliker, Paoli, Peterlongo, Piro, Porter, Rasmussen, Rees, Reinert, Renard, Robertsen, Rosen, Ruscheweyh, Sarwal, Segata, Seiler, Shi, Sun, Sunagawa, Sørensen, Thomas, Tong, Trajkovski, Tremblay, Uritskiy, Vicedomini, Wang, Wang, Wang, Warren, Willassen, Yelick, You, Zeller, Zhao, Zhu, Zhu, Garrido-Oter, Gastmeier, Hacquard, Häußler, Khaledi, Maechler, Mesny, Radutoiu, Schulze-Lefert, Smit, Strowig, Bremges, Sczyrba, McHardy. Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature Methods. 2022;19(4):429-440en_US
dc.identifier.cristinIDFRIDAID 2031232
dc.identifier.doi10.1038/s41592-022-01431-4
dc.identifier.issn1548-7091
dc.identifier.issn1548-7105
dc.identifier.urihttps://hdl.handle.net/10037/26204
dc.language.isoengen_US
dc.publisherNatureen_US
dc.relation.journalNature Methods
dc.relation.projectIDinfo:eu-repo/grantAgreement/EC/EXCELLENT SCIENCE/815962/EU/Microbiota-host interactions for integrative metabolic health reprogramming/Healthybiota/en_US
dc.rights.accessRightsopenAccessen_US
dc.rights.holderCopyright 2022 The Author(s)en_US
dc.titleCritical Assessment of Metagenome Interpretation: the second round of challengesen_US
dc.type.versionpublishedVersionen_US
dc.typeJournal articleen_US
dc.typeTidsskriftartikkelen_US
dc.typePeer revieweden_US


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