TL:DR If you are interested in calling indels with GATK, check out the below. If not, don’t. ——————————————————– So, this annoying guy asked me to add an analysis of indels* to a paper that has been itching to get off my desk for months. I finally got around to doing this, so thought I would…

TL:DR If you are interested in linking postcode and constituency, see 2015.04.03.postcode_to_constituency_lookup.tsv.gz in this git repo. You can then link constituency with demographic info here I was impressed by the Democratic Dashboard website recently. You pop in your postcode and it tells you lots of info about your electoral constituency, the demographic make up, as well as the…

I was just asked for some advice on PhD viva, so have turned the email into a blog post. —————— They often start by asking you to place your work into context of existing literature and summarise your main findings in 5-10 minutes, so have your summary ready. The main prep I did was to…

The WordPress.com stats helper monkeys prepared a 2014 annual report for this blog. Here’s an excerpt: The concert hall at the Sydney Opera House holds 2,700 people. This blog was viewed about 10,000 times in 2014. If it were a concert at Sydney Opera House, it would take about 4 sold-out performances for that many…

TL:DR? Lighter is an excellent sequencing read error correction tool, fast (90 seconds for 700 mb unzippped fastq) and well engineered (install was completely painless) It significantly speeds up assembly – 20% in my quick benchmark using a Salmonella genome It reduces the number of positions that have an AD ratio of <0.9, remember – every…

Exciting news everyone! Lauren Cowley is currently in Sierra Leone, being a Time Person of the Year, but she has still found time to write a blog post on her experiences – see below: ——————– I have been in Port Loko, Sierra Leone for 2 and a half weeks now. I’m working in the diagnostic lab…

I have just read Sean Eddy’s thought provoking blog post on the problems with how biology is handling high throughput sequencing which you should definitely read. One of his themes is that bioinformatics is going to be a key part of the 21st century biologists toolkit, and that biologists doing sequencing experiments should be able to tinker…

This post is about reproducing analysis from a paper, the first step in this is obviously get the data. In this case, the data is from the Sanger and the primary I’m interested in Salmonella Typhimurium ST313, a potentially invasive strain that is possibly in the process of genome reduction leading to human host restriction.…

I had two experiences recently that I’m sure many other people who use twitter have also had. I was reading about the poisson distribution and there was a great set of lecture notes from a Prof at Oxford University (which are on the first page of google results for ‘poisson distribution’). However, there seems to have…