I thought I would knock together a quick post listing a few useful introductory papers that I have sent to people on multiple occasions, just to save a bit of time. I will also include any suggestions that other people use to introduce others to the rapidly expanding world of bacterial genomic epidemiology. EDIT: going…
This is a post by Lauren Cowley. I have just spent one amazing month in Australia with Scott Beatson’s group at the University of Queensland. I was lucky enough to be awarded the Presidents fund grant by the SGM that enabled me to make the visit and am pleased with all the productive collaborations and…
I have a new job! A couple of weeks ago I became a permanent employee of PHE. This new role will mean a shift from VTEC O157 to Salmonella. We have sequenced 1500 strains of Salmonella from diverse serotypes to validate serotyping via MLST (see Achtman et al., 2013 for more details). This is prior…
Tanglegrams are a very cool way of visualising the difference between two trees. There is an implementation in Dendroscope that allows them to be made very easily, IF you know how (it isn’t covered very well in the documentation). This is how. This is definitely one of those, ‘write it down before I forget’ blogs.…
Tomorrow I’m going to Westminster Kingsway College in central London to talk to 11-18 year olds about careers in science, technology engineering and maths (STEM). The organisers have given us some questions the kids might ask and I thought that working through a few on here would help me get my thoughts together. I’m not…
As the final part of my assembly optimisation I was interested in the impact of Titus Brown’s Khmer/Diginorm approach on speed and quality. Ten samples (VTECs sequenced on GAII) were assembled with a variety of pipelines: SPAdes corrected fastqs, assembled with SPAdes Khmer-ed fastqs, SPAdes corrected, assembled with SPAdes SPAdes corrected fastqs, assembled with Velvet…
We have seen significant differences between assemblies of shiga toxigenic E. coli genomes where the DNA was extracted with different protocols. In those experiments, I used Velvet for assembly and I wanted to check whether the difference we were seeing between the different extraction methods was somehow a Velvet artefact. The recent GAGE-B paper showed…
As our project ramped up, we moved from a manual extraction method (Wizard) to a high throughput method (Qiasymphony). We thought that it would be prudent to check that the sequence data obtained by the two methods was equivalent. Therefore, on a GAII run of 96 strains we sequenced 72 isolates that had been extracted…
This post is by Lauren. Two weeks in Michigan by a lake in the spring time – bliss! PLUS I got to test out my bioinformatics skills and learn all the areas where I am severely lacking, this was really driven home to me when on the first day we were asked to do a…
Biologists often want to see annotated genomes so they can start digging into the genome using tools like Mauve and Artemis. First off though, I think it is really important to provide the ‘whole-y genome’ disclaimer (h/t Neil Perry). Before letting the biologist loose on the genome it is vital that they really meditate…
Bits and Bugs 