Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper
Fig 3
Detection of pathogen sequences in five synthetic patient RNA-seq datasets (Patient 1–5; rows), each with different levels of spiked-in viruses (EBV, HIV-1, U21941, and FR751039; columns), expected values shown as black vertical bars. As Centrifuge and Kraken2 are unable to delineate between the two HPV substrains (U21941 and FR751039), a combined count at the HPV level is tabulated.