Blog posts

2018

Carpentries-style computer practical for Molecular Epidemiology of Infectious Diseases

less than 1 minute read

Published:

As a Carpentries instructor and trainer I am familiar with the Carpentry lessons, especially with the Data Carpentry Genomics lesson for which I am one of the maintainers of the shell-genomics episode. However it was my first time using the new lesson template for university course lessons. These lessons have been given already in 2016 but needed an update. Here is the link to the new lessons.

2017

Popularity of SNP pipelines

2 minute read

Published:

Recently we got back a round of reviews on a small review paper. There was one sentence in the text were I listed some SNP pipelines that I thought were good examples. The topic of the review is not pipelines so the intention was not to list all, just one or two. However reviewer 2 did not agree with my choice of examples. He suggested to omit the name of the pipeline that was unpublished and name a few other published ones instead.

Poster ABPHM17

less than 1 minute read

Published:

Here’s the poster presented at ‘Applied Bioinformatics and Public Health Microbiology 2017’ at the Wellcome Genome Campus, Hinxton, Cambridge, UK on the Enterococcus faecium plasmidome

Drawing a tree with colored tips in R (ggtree)

1 minute read

Published:

ggtree is a R package designed for viewing and annotating phylogenetic trees. It is based on the ggplot2 package. Here I will show step-by-step how to draw a tree with colored tips, because, even thought the bioconductor documentation is clear and complete, I did not read about this very common visualization.