Wednesday, June 14, 2017

New Life in the Sanger Market

In my bit on "I'm not dead yet" technologies recently, I included large scale Sanger sequencing. That reflects to a large degree my personal experiences and biases.  Targeted Sanger is great for spot checking the occasional junction or misbehaving clone or strain, but I forget that many clinicians still see it as a gold standard.  Apparently there are others who disagree with me, as Thermo Fisher recently launched a new Sanger instrument targeted at small labs, and according to GenomeWeb Promega plans an instrument offering in the same space as well.

Tuesday, June 06, 2017

Ice Ghosts:A Shortage of Maps

I'm going to step outside the usual topic space here and cover an interesting but frustrating book I read partly on the flight to London Calling (which is about the only connection it has to genomics).  Ice Ghosts, by Paul Watson, covers the searches for the lost Franklin Expedition, a mid-1800s British Navy attempt to find the Northwest Passage.  It's a pretty good book, after all it did win a Pulitzer Prize,  The topic is thrilling: explorers under difficult conditions and a mystery that lasted over a century.  There are lessons for science in general, such as the value in carefully evaluating oral histories that some would discard as unreliable. But what is maddening for me is that in a book for which a central theme is poorly understood geographies and their interpretations, the set of supplied maps fail miserably at assisting in the telling of the story.

Monday, May 22, 2017

What Is (and Is Not) Sequence Assembly?

In the closing talk of the pre-London Calling workshop, Hans Jansen had closed his presentation with a question whether at some future date sequence assembly would become obsolete.  This was meant to be an aspirational vision for a distance timepoint, but one correspondent on Twitter saw it as hype.  I got in a bit of a discussion, constrained by the dreaded 140 character limit, which ended up largely illustrating that I have a somewhat more restricted definition of assembly than some people.  I'm going to explore this and you can judge for yourself

Thursday, May 18, 2017

London Calling 2017: Plant & Animal de novo Genomes

Okay, I'm desperately behind on writing up the external science from London Calling.  Not helpful that I claimed I would not only do so, but in multiple installments.  A number of the plenaries focused on large genome assembly, so that's what I'll tackle now -- plus a few other bits.   See also my Storify summaries, which include other reports on the conference.  Also check out my storifies on the SMRT Leiden conference, which ran at the beginning of the same week and discusses many similar topics.

Sunday, May 14, 2017

SFAF & I'm Not Dead Yet Technologies

Jonathan Jacobs posted his annual reminder that the Sequencing, Finishing and Analysis in the Future Meeting (SFAF) will be this week.  Alas, that meeting hasn't had many more tweeters in the past than Jonathan, but perhaps this year there will be more.  There's a glut of genomics conferences to track, compile tweets and opine on -- besides London Calling, there's been SMRT Leiden and Biology of Genomes, all in the span of two weeks!  This post is going to be a bit short on actual writing and more to just flag some talks at SFAF that grabbed my attention.  What I realized is that the talks at SFAF illustrate that a number of technologies I consider effectively dead retain significant attention.

Tuesday, May 09, 2017

London Calling 2017: A Theme of Consolidation

London Calling 2017 came to a close last Friday.  Any excuses of jet lag or nights running up ONT's bar tab won't hold up much longer, so time to finish this post (I really did start the night after Clive's talk!) I'm going to largely divide coverage on the dividing line of who presented: today's piece on Oxford Nanopore presentations, particularly Clive Brown's, and in the near future at least one focusing on the science users presented.  For other summaries of the action, I've created a storify of just blog posts and similar summaries of the meeting, as there were a great number (and I am on the hunt for additional ones I've missed)

Thursday, May 04, 2017

Nanopore Workshop Notes

I attended on Wednesday the London Calling pre-conference workshop, an add-on for those wishing for help getting started with MinION sequencing.  Judging from who I spoke to, many participants were utterly new to nanopore sequencing and more than a few were like me in that they had tried the platform and wanted to do better.  My colleague has gotten some very good results recently, which has re-fired my determination to get good at that myself.  Below are some limited notes I took that may be of general interest. Large portions of the workshop will go largely uncovered, as I focused on what was surprising or new.