An exploration of parameter settings for the recovery of pathogen reads in pure simulated viral samples.

Indexed samples include EBV, HIV-1, FR751039, U21941, and ERR2322364 (human RNA-seq sample). The viral samples are simulated to a depth of 100x genomic coverage. Each subsection of the table is the analysis for an individual sample, which has been searched with specified parameters. An example parameter string: k100s1m2000u_UniqRead, can be interpreted as k-mer length 100, step size 1, maximum occurrence 2000, uniqueKmer parameter turned on, and unique read flag turned on. For each of the queries (EBV, HIV-1, FR751039, U21941), the FlexTyper count in Single-end mode is listed. Last, the search time for retrieving k-mers from the index is listed in seconds. (XLSX)