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Table 3 Comparison of the classification accuracies using a real-world dataset

From: A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy

Taxonomy Level Method V1V2 Region
CST = 0.8 CST = 0.5
Species BLCA 0.570 0.716
Kraken 0.589 0.589
MEGAN 0.544 0.544
RDP 0.490 0.613
SPINGO 0.486 0.562
Genus BLCA 0.729 0.79
Kraken 0.694 0.694
MEGAN 0.745 0.745
RDP 0.643 0.708
SPINGO 0.605 0.650
Family BLCA 0.814 0.832
Kraken 0.777 0.777
MEGAN 0.869 0.869
RDP 0.775 0.805
SPINGO NA NA
  1. Each entry in the table shows the F-scores for a classifier (i.e., rows) based on all the OTU sequences in the msd16s dataset, as described in the main text. Two confidence score thresholds (CST), 0.8 and 0.5, were applied for BLCA, RDP Classifier, and SPINGO, the thresholds as in Table 1. Note that the SPINGO program does not produce family-level classification. In addition, Kraken and MEGAN do not provide any probabilistic-based parameters for evaluating the assigned taxa, thus we used their default taxonomic assignments for comparison