Harriet Dashnow

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Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significant challenges. Here we present SRST2, a read mapping-based tool for fast and accurate detection of genes, alleles and multi-locus sequence types(More)
[PB: When I read the title of this article I laughed out loud—how many times has that happened to you when reading professional articles? Laughter is good whatever the context. When I started the series in 2005, I had no idea it would be so successful. This article, which I had no part in writing, only adding commentary shown in italics, is in my mind a(More)
The mutation R403stop was found in an individual with mut(0) methylmalonic aciduria (MMA) which resulted from a single base change of C→T in exon 6 of the methylmalonyl-CoA mutase gene (producing a TGA stop codon). In order to accurately model the human MMA disorder we introduced this mutation onto the human methylmalonyl-CoA mutase locus of a bacterial(More)
The benefits of implementing high throughput sequencing in the clinic are quickly becoming apparent. However, few freely available bioinformatics pipelines have been built from the ground up with clinical genomics in mind. Here we present Cpipe, a pipeline designed specifically for clinical genetic disease diagnostics. Cpipe was developed by the Melbourne(More)
The benefits of implementing high throughput sequencing in the clinic are quickly becoming apparent. However, few freely available bioinformatics pipelines have been built from the ground up with clinical genomics in mind. Here we present Cpipe, a pipeline designed specifically for clinical genetic disease diagnostics. Cpipe was developed by the Melbourne(More)
# To whom correspondence should be addressed: kholt@unimelb.edu.au. CC-BY 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was. Abstract Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet(More)
'Big data' analytics can be defined by the requirement for flexible, high throughput computational analysis methods applied to large, heterogeneous datasets. We propose an architectural approach to 'big data' challenges in which the movement of data is minimized, and analysis methods are implemented on the data as portable services. We term this approach(More)
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