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dc.contributor.authorFritz, Adrian
dc.contributor.authorHofmann, Peter
dc.contributor.authorMajda, Stephan
dc.contributor.authorDahms, Eik
dc.contributor.authorDröge, Johannes
dc.contributor.authorFiedler, Jessika
dc.contributor.authorLesker, Till R
dc.contributor.authorBelmann, Peter
dc.contributor.authorDeMaere, Matthew Z
dc.contributor.authorDarling, Aaron E
dc.contributor.authorSczyrba, Alexander
dc.contributor.authorBremges, Andreas
dc.contributor.authorMcHardy, Alice C
dc.date.accessioned2019-02-25T14:01:35Z
dc.date.available2019-02-25T14:01:35Z
dc.date.issued2019-02-08
dc.identifier.citationMicrobiome. 2019 Feb 8;7(1):17. doi: 10.1186/s40168-019-0633-6.en_US
dc.identifier.issn2049-2618
dc.identifier.pmid30736849
dc.identifier.doi10.1186/s40168-019-0633-6
dc.identifier.urihttp://hdl.handle.net/10033/621702
dc.description.abstractShotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required. We describe the CAMISIM microbial community and metagenome simulator. The software can model different microbial abundance profiles, multi-sample time series, and differential abundance studies, includes real and simulated strain-level diversity, and generates second- and third-generation sequencing data from taxonomic profiles or de novo. Gold standards are created for sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. CAMSIM generated the benchmark data sets of the first CAMI challenge. For two simulated multi-sample data sets of the human and mouse gut microbiomes, we observed high functional congruence to the real data. As further applications, we investigated the effect of varying evolutionary genome divergence, sequencing depth, and read error profiles on two popular metagenome assemblers, MEGAHIT, and metaSPAdes, on several thousand small data sets generated with CAMISIM. CAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with standards of truth for method evaluation. All data sets and the software are freely available at https://github.com/CAMI-challenge/CAMISIM.en_US
dc.publisherBioMedCentralen_US
dc.rightsAttribution-NonCommercial-ShareAlike 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/*
dc.subjectBenchmarkingen_US
dc.subjectCAMIen_US
dc.subjectGenome binningen_US
dc.subjectMetagenome assemblyen_US
dc.subjectMetagenomics softwareen_US
dc.subjectMicrobial communityen_US
dc.subjectSimulationen_US
dc.subjectTaxonomic binningen_US
dc.subjectTaxonomic profilingen_US
dc.titleCAMISIM: simulating metagenomes and microbial communities.en_US
dc.typeArticleen_US
dc.contributor.departmentBRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56,38106 Braunschweig, Germany.en_US
dc.identifier.journalMicrobiomeen_US
refterms.dateFOA2019-02-25T14:01:35Z
dc.source.journaltitleMicrobiome


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