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 assemblies By now you probably heard about the new Nanopore technology, it is truly marvellous bit of engineering. The DNA strands are pulled through the…
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 positions that have been ignored due to low quality in some of your strains can be useful (i.e. use RAxML and…
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 present data when you want to express the relationship between different genotypes you have observed and…
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.…
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…
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 