Just back from Cheltenham Science Festival 2013 after giving a talk on bats and serial killers in ‘Just So Science’ in the Eureka tent. My colleague Chris Faulkes also spoke about naked mole-rats, and the audience also heard about Tasmanian devils, Burmese pythons and axolotls. Thanks to host Vivienne Parry, who presents the Radio 4 series ‘Just So Science’, for the invitation. The talk went well, and it was a gloriously sunny day – a fantastic trip.
Seminar at the Jodrell Laboratory, Royal Botanic Gardens at Kew today, on geographic profiling. A great place to visit, and some promising collaborations to explore. Another seminar tomorrow at Reading University, then a third at Durham University next Tuesday.
My new tattoo showing the Berlin Archaeopteryx!
Exciting announcement of a new dirt-cheap machine-less DNA sequencing technology. If their promises hold true, this technology will be a game-changer for those of us working with “emerging” non-model organisms because:
- it supposedly provide 100,000bp long reads. This will eliminate most scaffolding issues we have with assembling de novo genome sequence.
- using the USB thumb-chip version, no machine is required. Thus when you are out in the field, you can sequence right then and there – a potential workaround for worrying about tissue sample export permits… at least until new regulations appear!
High error rates are problematic in short reads because they introduce ambiguity making it challenging to align and assemble these reads. However, this is much less of an issue with longer reads: A 100,000bp region will remain uniquely identifiable even with Oxford Nanopore’s currently high error rate of 4%. And because for assembly you will use multiple reads representing the same region, error rate of assembled sequence will be low: if two reads overlap, your consensus sequence for the overlapping region will have an error of 4% * 4% = 0.16% (supposing that the errors give lower quality scores than normal sequence). If you have 3x coverage or more, you can resolve most errors unambiguously…
New year, new country, new job: I am now a Lecturer at Queen Mary University of London. I will continue to use genomics and bioinformatics approaches to examine the interplay between social evolution and genome evolution. Get in touch if you’re interested in working with me in a great place.
And a few nice papers on which I am coauthor are now out.
- PNAS: Relaxed selection is a precursor to the evolution of phenotypic plasticity. Led by Brendan Hunt at Georgia Tech
- Bioinformatics: Visualization and quality assessment of de novo genome assemblies – led by Oksana Riba-Grognuz – Source code available.
- Trends in Genetics: The genomic impact of 100 million years of social evolution in seven ant species. Reviews some of the findings from the ant genome projects & lays the foundation for coming analyses. Romain Libbrecht & I made the photo that was selected as cover image!