Microbiome & infection inequities

Subtitle: a series of sickening facts I’m interested in the role of the gut microbiome in infection, especially in settings with a high burden of infectious diseases. Therefore, I did a literature search on PubMed (full text of the search here). The search returned a total of 47 papers. What proportion do you think were…

Comparison of autoresearcher and ChatGPT-4 for literature review

I’m having a play around with some AI tools for literature searching and I came across the autoresearcher tool (link). Here is a comparison of the output of autoresearcher with ChatGPT4. TL;DR The question I asked both tools – “what is the role of the microbiome in mediating salmonella exposure outcomes?” autoresearcher output “The microbiome…

How to setup conda (April 2023 version)

There have been some recent changes to the conda/mamba ecosystem, see obligatory xkcd. This is my current way of creating a fresh install of conda. Setting libmamba as the conda solver should allow you mamba-like speed, while at the same time letting you just install programs like `conda install`.

Which pre-print servers accept narrative reviews?

This is a “blog it so I don’t have to ask again on twitter post”. We have a narrative review that we want to post as a pre-print, but Medrxiv/Biorxiv don’t accept them. I asked for pre-print servers that do accept narrative reviews on twitter, and these are the sites that were recommended: SciELO OSF…

Validation of SKA analysis for genomic epidemiology

TL;DR SKA is a high quality bioinformatics tool which enables you to rapidly do genomic epidemiology of very closely related isolates. SKA shows good correlation with traditional SNP calling techniques (BWA + GATK) SKA shows a consistent trend of identifying around 10 more SNPs between a sub-set of pairs of isolates than traditional method, I’m…

Basic options for bioinformatics data analysis

This post is written in the spirit of “if you write it in an email to more than one person, turn it into a blog”. It’s for beginners who are just starting out in bioinformatics and who need information about which path to go down for which programming language. ————————— Firstly, you will need to…

Parsing treebreaker output

Treebreaker is a nice piece of software which detects changes in the distribution of a phenotype across a phylogenetic tree. Code here. Paper here. In my case, I’m using it to find clades of lineage 4¬†M. tuberculosis¬†which are associated with East/Southeast Asia. It takes a phylogenetic tree and a phenotype file (the leaf labels and…