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Sequence analysis in R – GenEpi Day
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...
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Proportion plots – calculating proportion of pairwise comparisons that are...
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...
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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,...
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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...
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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...
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How to make a minimum spanning tree in bionumerics
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...
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Phylogenetic tree troubleshooting
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...
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Adventures with Nanopore
This is a guest post by Alex Jironkin (@biocomputerist) in the core bioinformatics group at Colindale. TL;DR: Try assembling your hybrid Illumina-MinION data with smaller number of kmers for better...
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