AMBER: Assessment of Metagenome BinnERs. Issue 6 (8th June 2018)

• Record Type: Journal Article
• Authors: Meyer, Fernando; Hofmann, Peter; Belmann, Peter; Garrido-Oter, Ruben; Fritz, Adrian; Sczyrba, Alexander; McHardy, Alice C
• Is Part Of: GigaScience. Volume 7:Issue 6(2018)
• Publication Date: 2018-06-08
• Subjects: binning -- metagenomics -- benchmarking -- performance metrics -- bioboxes; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1093/gigascience/giy069
• Languages: English
• ISSNs: 2047-217X

Abstract

Abstract: 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. However, assessing their quality is difficult due to the lack of evaluation software and standardized metrics. Here, we present Assessment of Metagenome BinnERs (AMBER), an evaluation package for the comparative assessment of genome reconstructions from metagenome benchmark datasets. 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 11 binning programs on two CAMI benchmark datasets. AMBER is implemented in Python and available under the Apache 2.0 license on GitHub.