JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale.

ABSTRACT: Transmission reconstruction-the inference of who infects whom in disease outbreaks-offers critical insights into how pathogens spread and provides opportunities for targeted control measures. We developed JUNIPER (Joint Underlying Network Inference for Phylogenetic and Epidemiological Reconstructions), a highly-scalable pathogen outbreak reconstruction tool that incorporates intrahost variation, incomplete sampling, and algorithmic parallelization. Central to JUNIPER is a statistical model for within-host variant frequencies observed by next generation sequencing, which we validated on a dataset of over 160,000 deep-sequenced SARS-CoV-2 genomes. Combining this within-host variation model with population-level evolutionary and transmission models, we developed a method for inferring phyloge

SUBMITTER: Specht I 

PROVIDER: S-EPMC11975037 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature