The introduction of new anti-viral medications has enabled an effort to reduce the burden of hepatitis C infections in the world. Molecular epidemiology investigations will be a major piece of elimination efforts. This dissertation introduces a distance based method to cluster hepatitis C cases likely to be close in the chain of transmissions. It also describes the Global Hepatitis Outbreak and Surveillance Technology (GHOST) which is based on the clustering method. Methods developed for quality assurance of GHOST input data and to methods scale the clustering method to data sizes relevant for GHOST.