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dc.contributor.authorBremges, Andreas
dc.contributor.authorFritz, Adrian
dc.contributor.authorMcHardy, Alice C
dc.date.accessioned2020-01-16T13:40:58Z
dc.date.available2020-01-16T13:40:58Z
dc.date.issued2020-01-01
dc.identifier.citationGigascience. 2020 Jan 1;9(1). pii: 5698015. doi: 10.1093/gigascience/giz154.en_US
dc.identifier.issn2047-217X
dc.identifier.pmid31909794
dc.identifier.doi10.1093/gigascience/giz154
dc.identifier.urihttp://hdl.handle.net/10033/622086
dc.description.abstractBACKGROUND: The number of microbial genome sequences is increasing exponentially, especially thanks to recent advances in recovering complete or near-complete genomes from metagenomes and single cells. Assigning reliable taxon labels to genomes is key and often a prerequisite for downstream analyses. FINDINGS: We introduce CAMITAX, a scalable and reproducible workflow for the taxonomic labelling of microbial genomes recovered from isolates, single cells, and metagenomes. CAMITAX combines genome distance-, 16S ribosomal RNA gene-, and gene homology-based taxonomic assignments with phylogenetic placement. It uses Nextflow to orchestrate reference databases and software containers and thus combines ease of installation and use with computational reproducibility. We evaluated the method on several hundred metagenome-assembled genomes with high-quality taxonomic annotations from the TARA Oceans project, and we show that the ensemble classification method in CAMITAX improved on all individual methods across tested ranks. CONCLUSIONS: While we initially developed CAMITAX to aid the Critical Assessment of Metagenome Interpretation (CAMI) initiative, it evolved into a comprehensive software package to reliably assign taxon labels to microbial genomes. CAMITAX is available under Apache License 2.0 at https://github.com/CAMI-challenge/CAMITAX.en_US
dc.language.isoenen_US
dc.publisherOxford Academicen_US
dc.rightsAttribution-NonCommercial-ShareAlike 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/*
dc.subjectCAMIen_US
dc.subjectDockeren_US
dc.subjectGenome Taxonomyen_US
dc.subjectNextflowen_US
dc.subjectPhylogenetic Placementen_US
dc.subjectReproducible Researchen_US
dc.titleCAMITAX: Taxon labels for microbial genomes.en_US
dc.typeArticleen_US
dc.contributor.departmentBRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56,38106 Braunschweig, Germany.en_US
dc.identifier.journalGigascienceen_US
refterms.dateFOA2020-01-16T13:40:59Z
dc.source.journaltitleGigaScience


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