Accuracy of HAYSTAC and other methods for a simple simulation.

Bar plot showing the mean count of false positives (red), false negatives (orange), and true detected species (blue) for two versions of the simple simulations dataset, each with two replicates: (A) without human DNA contamination (n = 2); and (B) with human DNA contamination (n = 2). The dotted line shows the number of simulated species in each set of samples (i.e., the maximum true positive; n = 10), and numbers above the error bars indicate the mean species count in each category. For the simulation without human contamination, HAYSTAC outperforms Kraken2/Bracken, KrakenUniq and MALT, and performs equally with Sigma (i.e., no false positives or false negatives). For the simulation with human contamination, HAYSTAC outperforms all four other methods. All of the 5 false positive species identified by HAYSTAC are known to contain human sequences in their reference genomes [37], confounding any analyses which do not explicitly filter human contamination.