New preprint from us! 🦠 Clinical metagenomics is great for sequencing pathogens directly from patient samples but for some protocols sensitivity for RNA viruses lags behind bacteria & fungi. We have shown why, and how to fix it. www.medrxiv.org/content/10.6...

Library preparation strategy critically impacts RNA virus sensitivity in clinical metagenomics

Clinical metagenomics uses sequencing for culture-independent identification of pathogens directly from clinical specimens. While a number of protocols claim to be pathogen agnostic, sensitivity for R...

medrxiv.org

New preprint from our Gates-funded Modjadji initiative showing that whole-genome surveillance of measles virus from wastewater greatly expands our ability for monitoring and control. Here, with our colleagues in South Africa - U.S., unfortunately, likely up next. www.medrxiv.org/content/10.6...

Integrating measles wastewater and clinical whole-genome sequencing enables high-resolution tracking of virus evolution and transmission

Measles outbreaks have surged globally in recent years, but current surveillance systems have limited capacity to monitor measles virus (MeV) transmission and evolution at population scale. Although M...

medrxiv.org

In light of recent P2 solo developments have dusted off an old image and updated it a little …….. 😉 @nanoporetech.com

Very excited to be using the soon-to-be released MK1D for HBV sequencing from Uganda!

For a few years I've been thinking about calling somatic mutations without matched normals using long read haplotypes. I've posted a preprint with my experiments to explore when this works (and when it doesn't) and developing a prototype mutation caller ("smrest"): www.biorxiv.org/content/10.1...