This study evaluates SNP calling pipelines' performance on bacterial data, finding that reference genome selection strongly impacts accuracy, with Snippy performing consistently well across diverse genomes.

GigaScience · Feb 1, 2020Peer-reviewedBioinformatics

Detection of viral pathogens with multiplex Nanopore MinION sequencing: be careful with cross-talk

Yifei Xu, Kuiama S. Lewandowski, Sheila Lumley, Steven T. Pullan, Richard Vipond, Miles W. Carroll, Dona Foster, Philippa Clare Matthews, Tim Peto, Derrick W. Crook

The paper assesses cross-talk in multiplex Nanopore MinION sequencing and finds 0.056% of reads are misassigned due to chimeric reads.

Frontiers in Microbiology · Sep 19, 2018Peer-reviewedBioinformatics

Human Herpes Virus 6 (HHV-6) - Pathogen or Passenger? A pilot study of clinical laboratory data and next generation sequencing

Colin Sharp, Tanya Golubchik, William F. Gregory, Anna L. McNaughton, Nicholas Gow, Mathyruban Selvaratnam, Alina Mirea, Dona Foster, Monique Andersson, Paul Klenerman, Katie Jeffery, Philippa C. Matthews

This study examines HHV-6 prevalence in clinical samples using PCR and NGS, finding 33% positivity in hematology patients and 20% detection via NGS in CSF and respiratory samples.

bioRxiv · Jul 5, 2018 · PreprintMicrobiology

Multiuse patient monitoring equipment as a risk factor for acquisition of Candida auris

Hilary Madder, Ian Moir, Ruth Moroney, Lisa Butcher, Robert Newnham, Mary Sunderland, Tiphanie Clarke, Dona Foster, Peter Hoffman, Ginny Moore, Colin S Brown, Katie JM Jeffery

The paper identifies multiuse patient monitoring equipment as a risk factor for acquiring Candida auris in a neurological intensive care unit.

bioRxiv · Jun 13, 2017 · PreprintMicrobiology