This repository contains all source code used during the PHA4GE project and all the report files generated during the Bioinformatics analysis. The report files were used to write the manuscript for this project titled Dissecting the Genomic Landscape and Virulence Arsenal of Klebsiella pneumoniae recovered from Environmental Reservoirs in Uganda.
The genome sequencing for this study was funded by the Public Health Alliance for Genomic Epidemiology (PHA4GE) grant (INV-038071) to support pathogen genomics data standards and bioinformatics interoperability awarded to Ivan Sserwadda. This study was nested within a bigger project titled “COVID-19 and Antimicrobial Resistance in East Africa (CARE) project” which was part of the Global Effort on COVID-19 (GECO) heath research program awarded by the UK Department of Health and Social Care (DHSC) through the National Institute for Health Research (NIHR) and the Medical Research Council (MRC) which is part of the UK Research and Innovation (UKRI).
The genomic raw reads files from this study are publicly available at the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) under the study BioProject ID PRJNA1234855.