How to do a Dendroscope tanglegram

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.…

Impact of Khmer/Diginorm on SPAdes and Velvet assembly

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…

Assembly difference due to DNA extraction method?

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…

Plot maps with R

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…

Annotating phylogenetic trees

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.…