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Data released on June 07, 2018

Supporting data for "AMBER: Assessment of Metagenome BinnERs"

Meyer, F; Hofmann, P; Belmann, P; Garrido-Oter, R; Fritz, A; Sczyrba, A; McHardy, A, C (2018): Supporting data for "AMBER: Assessment of Metagenome BinnERs" GigaScience Database. http://dx.doi.org/10.5524/100454 RIS BibTeX Text

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.

Contact Submitter

Additional information:

https://github.com/CAMI-challenge/AMBER

https://scicrunch.org/resolver/RRID:SCR_016151

https://cami-challenge.github.io/AMBER/

Keywords:

binning metagenomics benchmarking performance metrics bioboxes 

Software, Metagenomic

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Funding:

  • Funding body - Deutsche Forschungsgemeinschaft
  • Comment - Cluster of Excellence in Plant Sciences (CEPLAS)
  • Funding body - Helmholtz society

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File NameSample IDData TypeFile FormatSizeRelease Date 
mixed archivearchive479.68 KB2018-05-15
ReadmeTEXT1.41 KB2018-05-15
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