Fig. 2

Pathonoia reduces number of false positives (FP) in noisy metagenomic samples. A The spectrum of species is shown, as reported by Kraken 2 and Pathonoia for a cell line sample infected with Human Herpes Virus (HHV). The top 10 most abundant species are highlighted. Kraken 2 reported 7262 organisms of which 250 are shown that have \(>100\) reads. Pathonoia lists 132 organisms and Herpes viruses ascend in the ranking of reported species. B Number of reported species in two datasets (12 and 24 samples) by Kraken 2, Pathonoia and Kraken with threshold (organism detected if \(>100\) reads counted). A lower number of detected organisms is desirable since it reduces the number of FP. C Pathonoia aims to improve the precision of detected organisms in a sample. FP (sequencing errors, other sample bias or random alignments, especially with poor quality reads) should be removed. D Average precision, recall and F1 for a simulated dataset, evaluated for Kraken 2-based algorithms and Centrifuge. Recall is the highest in Kraken 2 and Centrifuge. With removing FP from the Kraken results, every algorithm also loses some TP (recall goes down). E Number of species detected in simulated dataset. High recall in D is explainable by the high number of species that each algorithm finds