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.
Highlights
Metagenomics allows studying microbial communities and their members by shotgun sequencing
To demonstrate an application of AMBER, we performed an evaluation of the genome binning submissions to the first Critical Assessment of Metagenome Interpretation (CAMI) challenge, together with predictions from four more programs and new program versions, on two of the three challenge data sets
These are simulated benchmark data sets representing a single sample data set from a low complexity microbial community with 40 genomes and a 5-sample time series data set of a high complexity microbial community with 596 genome members
Summary
Metagenomics allows studying microbial communities and their members by shotgun sequencing. Following community requirements and suggestions, the first CAMI challenge provided metagenome data sets of microbial communities with different organismal complexities, for which participants could submit their assembly, taxonomic and genomic binning, and taxonomic profiling results. These were subsequently evaluated, using metrics selected by the community [1]. We describe AMBER (Assessment of Metagenome BinnERs), an evaluation package for the comparative assessment of genome binning reconstructions from metagenome benchmark data sets It implements all metrics decided by the community to be most relevant for assessing the quality of genome reconstructions in the first CAMI challenge and is applicable to arbitrary benchmark data sets. It complements the popular CheckM software that assesses genome bin quality on real metagenome samples based on sets of single-copy marker genes[3]
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