TL;DR Pseudofinder run using the bakta database has a good sensitivity and decent postive predictive value for detecting pseudogenes. Pseudofinder run with the bakta database can differentiate between gastrointestinal and extraintestinal Salmonella when you look at degradation of the central anaerobic metabolism genes. Main I’m interested in identifying pseudogenes (also, and maybe more properly, known…
I recently ran RGI on some gut microbiome samples, and I wanted to compare the prevalence of extended spectrum beta-lactamase (ESBL) genes between some of the groups in my study. This wasn’t listed directly in the RGI output, so I needed to add that info in. I asked around and found 3 solutions: The information…
Subtitle: a series of sickening facts I’m interested in the role of the gut microbiome in infection, especially in countries with a high burden of infectious diseases such as Malawi. Therefore, I did a literature search on PubMed for papers on the microbiome from these kinds of country (full text of the search here). The…
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 autoresearcher will include literature citations for its output, which is nice because ChatGPT currently cannot do this. However, based on my subjective view…
I was interested in getting a list of countries with a “high burden of infectious diseases”. From googling around, I found this nice image from Our World in Data (I love them! Source, with CSV etc). The underlying data from this comes from the Global Burden of Disease (GBD) initiative at the Institute of Health…
For some unfathomable reason some journals (e.g. Lancet journals) require you to use floating decimal places instead of normal ones. This is a real pain to do, because you can’t just do a find and replace because that would also replace the full stops. This is an opportunity to use a regex! ChatGPT tells us…
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`. wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-x86_64.sh conda update…
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…
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…
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…
Credit for this post is really due to Peter van Heusden, Torsten Seemann, (and Anders Gonvalces Da Silva has had lots of useful discussions with Torsten about this issue), Conor Meehan and Leonardo de Oliveira Martins. TL:DR Two ways to easily give IQ-TREE the number of constant sites: From Leo – For whole genome phylogenetic…
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…
I just spent an amazing three days motorbiking round the Ha Giang loop in northern Vietnam. Fantastic thing to do, just mind blowingly amazingly spectacular. However, I had a bit of a stressful time making the connection between my plane arriving into Noi Ba airport and the bus to Ha Giang, but it all worked…
It’s a truth universally acknowledged, that for a research career to flourish you need to publish first author papers. However, like many things concerning scientific publishing, this norm fails the ‘explain it to a non-biologist’ test. Non-biologist: So, how do you get credit for the papers you publish? Biologist: Well, if you are listed first…
I saw this amazing ‘natures-heartbeat‘ cartogram, and thought it would be cool to have something similar for TB incdience. There doesn’t seem to be any TB cartograms already available, so I thought I would make my own. I used the cartogram package in R. After spending some time in the deeper circles of R dependecy…
