So, I’m supposed to be writing my speech for my brothers wedding which is a week today (EDIT: which went very well, thanks for asking ;-), mazel tov James and Morgan), but I thought it would help me get in the zone to write a quick blog post. Hopefully I will remember not to put…
TL;DR HelixIO is a slick platform for telling you what is in your fastq sample – very useful for microbiologists! Will be interesting to see how it stacks up against KmerID in a larger number of samples. Interesting ycombinator thread HelixIO have recently launched a public beta of their intriguing bioinformatics platform for ‘fast, portable…
I think some biologists have a bit of a blind spot for bioinformatics when it comes to critical thinking. There may be a bit of a ‘well, the computer says this, therefore it is true’ attitude. I think that any biologist who is interacting with bioinformatics/NGS results should take the following steps: 1. Take a…
Or, how I failed advanced file copying. TL:DR? Phylogenetic trees can be hard to interpret – use bootstraps to help! Low coverage in one strain or having an outlier can screw with your tree Including positions that have been ignored due to low quality in some of your strains can be useful (i.e. use RAxML and…
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…
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…
A week or two ago I went to an interesting meeting about the clinical bioinformatics training scheme. This is a clinical scientist training programme, akin to those that train clinical geneticists and microbiologists. The first cohort of 13 students are currently making their way through the scheme. I had a look through the curriculum after the…
This is a blog post by Lauren Cowley ——————————————————————————— TL;DR? A confusing difference in trimmed/non-trimmed velvet phage assemblies raised suspicions that it was a mixed phage culture Spades assembly seemed to show more than one phage present in the culture I concluded that spades is better than velvet at showing a representation of the whole…
This is a ‘write it down before I forget’ post. I have shared it in case anyone else is overcome by a sense of existential dread at having to use Bionumerics. Minimum spanning trees are a nice way to present data when you want to express the relationship between different genotypes you have observed and…
This post will be a short summary of an interesting paper by Michael McClelland’s group, Evolutionary genomics of Salmonella enterica subspecies, Desai et al., 2011. I will focus on the phylogenetic aspects of the study as this is my primary interest at the moment. Intro 6 sub-species of Salmonella enterica, 5/6 of which (excluding enterica…
Bits and Bugs 