Abstract: Various embodiments disclosed relate to a method of quality control for a biological sample. The method can include receiving genetic data sequenced from the biological sample, determining whether an endogenous control is apparent in the genetic data, and in the event that the endogenous control is apparent in the genetic data, determining whether the biological sample is contaminated. The genetic data can be analyzed for sequences from both pathogen genetic material and mitochondrial genetic material. The endogenous control can be determined based on whether at least a threshold amount of the genetic data includes sequences for the mitochondrial genetic material.

Abstract: Various embodiments disclosed relate to a method for detection of coinfection of two or more pathogen variants in an individual. The present disclosure includes methods of receiving a biological sample, selecting a first variant of the pathogen and a second variant of the pathogen, sequencing the biological sample, calculating a composite alternative allele fraction, and if the sample is a mixed sample, searching individual reads to detect a recombinant pathogen.