Sequencing instruments by number
A quick one: I made this plot earlier today for a presentation. The data is from our Omicsmaps site which I curate with James Hadfield. Didn’t actually use it in the end but thought I’d post it in case it was useful for someone. Notable is the rise in HiSeq reciprocated by the decline in [...]
Adaptor trim or die: Experiences with Nextera libraries
One of the first posts I did on this blog, way back in September 2009 was about my experiences with filtering and trimming Illumina sequences, and it proved rather popular. To date, it has been viewed a whopping 8,560 times! But funnily enough, since that post was written my attitude towards filtering Illumina data slowly [...]
Balti and Bioinformatics: Midlands Sequencing and Bioinformatics Meeting: Monday, 20th May 2013
It’s that time again! Balti and bioinformatics will return .. on Monday, 20th May 2013. Not dissimilar to last time, we will feature complimentary samosas from Smethwick’s finest sweet shop, and hopefully without the bit where about 40 people had to crowd into my office. Spaces will be limited, please register to attend via the [...]
Goodbye and thank you to Birmingham!
Well, today is my last working day at the University of Birmingham, before I set off after Easter for a new position at the University of Warwick as Professor of Microbial Genomics and Head of a new Division of Microbiology and Infection in Warwick Medical School. I have been at the University of Birmingham since [...]
Crowd-sourcing killer outbreaks: Nice video from the BBSRC and Arran Frood
The BBSRC have done a nice job making a short video about the E. coli O104:H4 outbreak crowd-sourcing project, featuring little old me as well as the far more telegenic Lisa Crossman. Check it out, it’s got some spooky music too. Also please check out the OpenAshDieBack crowd-sourcing project currently ongoing, coordinated by the chaps [...]
A chat with Oxford Nanopore’s Clive Brown at AGBT 2013
Don’t judge me, reader, because I’d skipped a session at AGBT to go and have a swim in the sea. A man can only spend so much time in dimly-lit, low-ceilinged hotel conference rooms, popping low-sugar sweets, before the will to live ebbs away. On returning to the conference, passing the bar I spotted a [...]
Applied Bioinformatics & Public Health Microbiology: 15 – 17 May 2013
The awesome ABPHM meeting is back in 2013! This is a really nice conference that I am very happy to help organise. It’s a bit different from other public health microbiology conferences in that it specifically aims to bring together public health microbiologists and epidemiologists with bioinformaticians. Once we have everyone in the same room, [...]
Loman’s law of bioinformatics
Loman’s law of bioinformatics states: If you haven’t found at least one serious bug in the bioinformatics pipeline you are re-using then you don’t yet understand it. Loman’s second law of pipelines: By the time you’ve got someone elses pipeline working to your satisfaction you could have written your own.
Sequencing data: I want the truth! (You can’t handle the truth!)
Two sequencing papers caught my eye this week. This letter from Piskol and Li is perhaps the final nail in the coffin for the heavily criticised and debunked (also see: GenomesUnzipped) RNA editing paper from Li and Cheung published in Science in early 2011 (as Thomas Keane said on Twitter: ‘I can’t believe people are still debating this!). The letter Piskol and Li examined [...]