Abstract: The present disclosure provides methods and systems for detecting active microbial infection. In some cases, the methods can be used to detect active infection in a recipient of a transplanted organ, graft, or medical device. The present disclosure provides a method of monitoring disease in a human subject, wherein the method comprises obtaining a biological sample from the human subject; measuring concentrations of microbial cell-free nucleic acid (mcfNA) in the biological sample; comparing sequencing coverage near the origin of replication of a microbe to coverage in later replicating regions to derive a peak-to-trough ratio (PTR) score; and based at least on the PTR score, determining a rate of replication of the microbe. The methods described herein may analyze fragment lengths.

Abstract: Provided herein are direct-to-library methods, systems, and compositions.

Abstract: Provided herein are fragment length profiles of nucleic acid libraries, methods of generating fragment length profiles of nucleic acid libraries and methods of using fragment length profiles for diagnostics and/or prognostics. The application further provides methods, compositions and kits for determining the infection stage or the site of localization in a subject.