I’m reading an interesting article which Marc Lipsitch tweeted about. The C-Word: Scientific Euphemisms Do Not Improve Causal Inference From Observational Data by Miguel Hernan. The main take-away messages for me are that Almost all scientific studies are aiming for causal inference, but people working on non-intervention, non-randomised studies (aka association/descriptive/exploratory studies) are generally discouraged from…

Here, in the interests of ‘if you have to email it twice, write a blog’ is my high-level overview of what a bacterial genomics pipeline looks like. 1. quality assess fastqs with e.g. fastqc, visualise these across your dataset with MultiQC. If data is particularly bad, do quality trimming, if not, then don’t. 2. do species…