Chimera detection pipeline. Red arrows represent unaligned reads. Black arrows represent aligned reads and data. This figure outlines the standard computational subtraction pipeline used to generate SummonChimera input. Mapping of paired-end reads must occur to a database composed of both virus and humangenomes with Bowtie2. The BLASTN steps are ordered for optimal search time. Read counts at each step of the pipeline for each sample can be found in Additional file 1.