Source code repository for the paper "Genomic Surveillance of SARS-CoV-2 in the Bronx Enables Clinical and Epidemiological Inference"
The folder covid_bronx/ is a python package containing functions used by the scripts in the scripts/ folder. The artic/ folder contains scripts for running the artic/ pipeline.
Please contact Saad Khan (@smk508 / skhan8 at mail dot einstein dot yu dot edu) with any questions.