ecthomson/Contamination-Phylogeny: Contamination-Phylogeny v1.0

Release of code used in: Uncovering Tthe viral aetiology of undiagnosed acute febrile illness in Uganda using metagenomic sequencing Shirin Ashraf1, Hanna Jerome1, Daniel Lule Bugembe2,3, Deogratius Ssemwanga2,3, Timothy Byaruhangaa,2, John Timothy Kayiwa2, Robert Downing2, Jesus F. Salazar-Gonzalezb,3, Maria G. Salazar3, James G. Shepherd1, Craig Wilkie4Wilkie4, Chris Davis1, Nicola Logan1, Vattipally B. Sreenu1, Gavin S. Wilkie1, Ana da Silva Filipe1, Alfred Ssekagiri1, 2, Prossy Namuwulya1,2, Henry Bukenya2, Brian K. Kigozi2, Weronika Witkowska McConnell1, Brian J. Willett1, Stephen Balinandi2, Julius Lutwama2, Pontiano Kaleebu2,3, Josephine BwogiϮ2, Emma C. ThomsonϮ1,5Ϯ5 These authors Ccontributed equally Ϯ These authors Ccontributed equally ** Corresponding authors: Emma Thomson emma.thomson@glasgow.ac.uk and Josephine Bwogi jbwogi@uvri.go.ug AffiliationsInstitutions 1 MRC-University of Glasgow Centre for Virus Research, UK (CVR) 2 Uganda Virus Research Institute, Uganda (UVRI) 3 MRC/UVRI & LSHTM Uganda Research Unit, Uganda (MRC-UVRI) 4 School of Mathematics and Statistics, University of Glasgow, UK 5 5 London School of Hygiene and Tropical Medicine, UK (LSHTM)