Gaia2.0_benchmark
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Recent publications have benchmarked current 16S and shotgun pipelines to analyze metagenomics data:
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McIntyre, et al. 2017
doi: 10.1186/s13059-017-1299-7
whole genome sequencing
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Siegwald, et al. 2017
doi: 10.1371/journal.pone.0169563
amplicon sequencing, 16S rRNA
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The same datasets used for the benchmark were analyzed with GAIA, thus calculating its precision, recall and F-measure.
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The precision, recall and F-measure for the other pipelines were extracted from the publications.
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Please find the different datasheets with the benchmarking results below:
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- WGS-species
Results using the whole genome sequencing datasets from Segata et al., 2013 and Ounit and Lonardi, 2016
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- rRNA-family
Results using the 16S amplicon sequencing datasets from Siegwald, et al. at family taxonomic level
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- rRNA-genus
Results using the 16S amplicon sequencing datasets from Siegwald, et al. at genus taxonomic level
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