The global burden of infectious disease has declined in recent decades. Yet, patients who are immunocompromised and individuals in resource-limited settings remain at high risk of infection. In this dissertation, I will present several next generation sequencing assays that we have created that enable new ways to monitor and study infectious diseases. I will present two classes of technologies that target two different analytes: (1) cell-free DNA (cfDNA) in biological fluids and (2) viral transcripts within single cells. We have developed a library preparation assay that is sensitive to ultrashort cfDNA, which captures information about the pathogen and host. We applied this cfDNA sequencing assay to a large number of urine samples collected from patients with viral and bacterial urinary tract infections. Our findings indicate cfDNA sequencing can accurately detect a broad range of uropathogens and describe functional information about the infectious agent and host. We have also developed a complementary analytical pipeline to reduce false-positive identifications and background contamination. We have recently applied this pipeline in the monitoring of infectious diseases that are endemic in low-income countries. Using DNA sequencing, we proved that genome replication dynamics can be observed during MTB infections and that an abundance of enteric bacteria is present in the plasma of children suffering environmental enteropathy. In the second part of the dissertation, I will introduce a new high-throughput single-cell RNA sequencing tool that combines enrichment measurements of targeted RNA sequences with unbiased profiling of the polyadenylated transcriptome across thousands of single cells in the same biological sample. We applied this technique to simultaneously characterize the non-A-tailed transcripts of a segmented dsRNA viruses and the transcriptome of the infected cells. In addition, we applied the technology to simultaneously determine the natively paired, variable region heavy and light chain amplicons and the transcriptome of B lymphocytes. In summary, we have created new tools to capture and sequence nucleic acids in biological fluids and single cells, thereby providing novel ways to understand pathogens as well as host immunity and damage.