Fig. 4

Benchmarking of amplicon sequence data analysis pipeline’s performance using a mock community with known species composition. A Accuracy of each pipeline in predicting the mock community composition at genus level. For benchmarking we compared the fraction of reads assigned to true genera and both correctly and erroneously recovered genera. Precision, Recall, and F-score were calculated based on the true positive, false positive, and false negative taxa identified. At species level, LotuS2 excelled also in these statistics (Supplementary Figure S9). B Percentage of true positive ASVs/OTUs having a nucleotide identity ≥ indicated thresholds to 16S rRNA gene sequences of genomes from the mock community. Pipeline(s) showing the highest performance in each comparison is denoted with a star (*). TP, true positive; ASV, amplicon sequencing variant; OTU, operational taxonomic unit. LotuS2-UPARSE and LotuS2-VSEARCH had the same result, therefore colors are overlaid