PathSeq: software to identify or discover microbes by deep sequencing of human tissue

Many human diseases are believed to be caused by undiscovered pathogens1–3. The advent of next-generation sequencing technology presents an unprecedented opportunity to identify pathogens in hitherto idiopathic diseases. Here we present PathSeq, a highly scalable software tool that performs computational subtraction on high-throughput sequencing data to identify non-human nucleic acids that may indicate candidate microbes. PathSeq exhibits high sensitivity and specificity in its ability to discriminate human from non-human sequences using both simulated and experimental transcriptome and whole-genome sequencing data. PathSeq is implemented in a cloud computing environment making it readily accessible by the scientific community.