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 