Bits and Bugs

Applying bioinformatics to public health microbiology

Salmonella

IPython notebook of Salmonella e-burst groups

I thought it might be fun to knock up a quick IPython notebook with some information about the number of e-burst groups (eBGs) within some of the more common (in the UK) Salmonella serotypes. At the moment, it can only be statically rendered, via a github gist and the IPython notebook viewer. Might look further into hosting…

April 17, 2014 in Bioinformatics, Microbiology, Salmonella.

Sequence type of Salmonella enterica subsp. I reference genomes

As part of the on-going rollout of WGS at PHE, we needed to know the MLST Sequence Type (ST) of the completed Salmonella reference genomes. However, this info was not that easy to come across either in the literature or the Salmonella MLSTdb. I deteremined the ST of these genomes by converting the completed sequence…

April 4, 2014 in Microbiology, Salmonella.

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