Cheltenham Science Festival 2013

Me outside the Eureka tent before my talk

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 Jodrell Laboratory

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.

Oxford Nanopore sequencing – a revolution for non-model organisms?

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!

MinionUSBThumbchipSequencer

 

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 publications & new job!

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.

Queen mary qmul logo blue

And a few nice papers on which I am coauthor are now out.

TIGs ant genomes