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…
Another thing I have learned to do while at HSPH is to make maps with a nice sprinkling of visual sugar e.g. proportional point sizes, different colours, different shapes. This post will take you through that. Thanks to Amy Wesolowski at HSPH for teaching me how to do this! The commands below can also be downloaded…
Once your phylogenetic tree gets above 50-100 strains it can become a bit unwieldy to analyse. One nice way of getting around this is to annotate your tree with relevant info e.g. serotype, phage type, source, date, location etc. A while ago, Tim wrote a script to annotate NEXUS format trees for viewing in e.g.…
I got a PHE fellowship to come and visit Bill Hanage at the Harvard School of Public Health. While I was going to rely on my English accent to convince everyone I’m intelligent, half the people in the group are English so I thought I better do some work. One of the English expats is…
We, like many people, are interested in optimal de novo genome assembly. When you assemble a genome you want the best possible representation of the ‘true’ genome. How can we obtain the best possible representation? In the past we have used VelvetOptimiser to do our assemblies. This assembles with a range of k-mers and returns…
I attended the GenEpi Day at London School of Hygeine and Tropical Medicine on Wednesday (would highly recommend attending if they run it again). For me, there were a couple of highlights – Ed Feil’s talk and the use of R for sequence analysis. This post will be about the use of R for sequence…
Bits and Bugs 