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AMBER: Assessment of Metagenome BinnERs

By Fernando Meyer, Peter Hofmann, Peter Belmann, Ruben Garrido-Oter, Adrian Fritz, Alexander Sczyrba, Alice C. McHardy

Posted 25 Dec 2017
bioRxiv DOI: 10.1101/239582 (published DOI: 10.1093/gigascience/giy069)

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 ten different binnings 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).

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