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Authors
Meyer, FernandoHofmann, Peter
Belmann, Peter
Garrido-Oter, Ruben
Fritz, Adrian
Sczyrba, Alexander
McHardy, Alice C
Issue Date
2018-06-08
Metadata
Show full item recordAbstract
Reconstructing the genomes of microbial community members is key to the interpretation of shotgun metagenome samples. Genome binning programs deconvolute reads or assembled contigs of such samples into individual bins, but assessing their quality is difficult due to the lack of evaluation software and standardized metrics. We present AMBER, an evaluation package for the comparative assessment of genome reconstructions from metagenome benchmark data sets. It calculates the performance metrics and comparative visualizations used in the first benchmarking challenge of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). As an application, we show the outputs of AMBER for eleven different binning programs on two CAMI benchmark data sets. AMBER is implemented in Python and available under the Apache 2.0 license on GitHub (https://github.com/CAMI-challenge/AMBER).Affiliation
BRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56, 38106 Braunschweig, Germany.PubMed ID
29893851Type
ArticleISSN
2047-217Xae974a485f413a2113503eed53cd6c53
10.1093/gigascience/giy069
Scopus Count
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- Creative Commons
Except where otherwise noted, this item's license is described as Attribution-NonCommercial-ShareAlike 3.0 United States