Supporting data for "AMBER: Assessment of Metagenome BinnERs"

Dataset type: Metagenomic, Software
Data released on June 07, 2018

Meyer F; Hofmann P; Belmann P; Garrido-Oter R; Fritz A; Sczyrba A; McHardy AC (2018): Supporting data for "AMBER: Assessment of Metagenome BinnERs" GigaScience Database.


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.

Additional details

Read the peer-reviewed publication(s):

Meyer, F., Hofmann, P., Belmann, P., Garrido-Oter, R., Fritz, A., Sczyrba, A., & McHardy, A. C. (2018). AMBER: Assessment of Metagenome BinnERs. GigaScience, 7(6). doi:10.1093/gigascience/giy069

Additional information:

File NameSample IDData TypeFile FormatSizeRelease Date 
mixed archivearchive479.68 KB2018-05-15
ReadmeTEXT1.41 KB2018-05-15
Displaying 1-2 of 2 File(s).
Funding body Awardee Award ID Comments
Deutsche Forschungsgemeinschaft Cluster of Excellence in Plant Sciences (CEPLAS)
Helmholtz society
Date Action
June 7, 2018 Submitter updated from : Alice McHardy
June 7, 2018 Dataset publish
June 15, 2018 File readme.txt updated
June 15, 2018 readme.txt: file attribute updated
June 15, 2018 File readme.txt updated
July 9, 2018 Manuscript Link added : 10.1093/gigascience/giy069