Determining the composition of bacterial communities at strain level resolution is critical for many applications in infectious disease epidemiology and in bacterial ecology.
Using the latest advances in computational inference and sequence analysis, an international team involving close collaboration with leading institutions on bacterial genomics, including the Wellcome Sanger Institute and University of Oxford, led by professors Jukka Corander and Antti Honkela (both in FCAI) has developed a new metagenomics tool called mSWEEP, which goes significantly beyond the state of the art in this field.
The effectiveness of mSWEEP is demonstrated with infection data from major human pathogens and it is expected to pave the way for entirely new approaches to addressing important biological and clinical questions about inter-strain competition, dissemination of resistance and virulence.
The research article: High-resolution sweep metagenomics using ultrafast read mapping and inference.