Sunday, December 18, 2016

Sequencer Archaeology

One of the frustrating side effects of outsourcing all your sequencing is that lack of connection to the actual machines.   Rarely have I gotten to visit sequencing labs, and the only time I've seen one with the cover open was when a Polonator was being shown off at a conference.  So it was a lot of fun to watch an almost hour-long YouTube video that Lex Nederbragt had pointed out in which someone who likes to disassemble complicated electronics performs his craft on a 454 FLX.

Thursday, December 15, 2016

Roche Abruptly Breaks Off PacBio Partnership

This morning was a solid block of meetings, but in a pause I checked my phone and saw the shocking headline: Roche Diagnostics had suddenly terminated their partnership with Pacific Biosciences to commercialize the Sequel instrument for clinical applications. Based on the few things I've read and a conversation with Bio-IT World's Allison Profitt, I've formed a few ideas, but certainly still find this a bit mystifying.  Perhaps the first part of next year, with the JP Morgan Conference and AGBT, will see Roche revealing a bit more about why they decided to break up with their partner.  Particularly when Roche had already made all their milestone payments; going forward

Wednesday, December 14, 2016

Let's Stop Talking Consensus Accuracy

A common approach for comparing sequencing platforms and assemblies is to report the consensus accuracy, just as for the platforms themselves the raw read accuracy is often reported.  I'm going to go on record with my opinion that stating these as "99.9% accurate" is a terrible habit which must be kicked, as it interferes with proper comparisons.

Friday, December 09, 2016

Siddhartha Mukherjee's The Gene, An Intimate History & the Crafting of Scientific Stories

Back in 2011,  I read and reviewed Dr. Siddhartha Mukherjee's book on the history of cancer therapy, The Emperor of All Maladies.  I liked the book, but as is my character I also listed some criticisms.  It was a very pleasant surprise to one day discover an email from Dr. Mukherjee engaging me on my points.  A real author, writing me!  Fast forward to this fall, and I had some inexplicable inertia to reading his new book, The Gene, An Intimate History.  This time he drove the process forward, asking if I'd like to read and review the book and if so could his publisher send me a copy?  Wow!  Having just finished the book, here goes the full review.

Tuesday, December 06, 2016

Reversible Terminators: Not Just For Sequencing

Reversible terminator nucleotides lie at the heart of sequencing-by-synthesis systems such as Illumina.  These nucleotides in their original state cannot be extended, terminating DNA polymerization.  But with the correct chemical treatment, the block is removed and polymerization can continue.  A recent paper moves the concept from sequencing to making large single mutation libraries.  The authors have apparently also applied for a patent (according to the Conflicts of Interest statement accompanying the paper), though that does not turn up on Google.

Friday, December 02, 2016

Oxford Nanopore New York City Meeting, Day 2

The second and final day of Oxford Nanopore's New York User Meeting ran today.  I've again been mining tweets, since I wasn't on site.  Oxford itself has posted a summary of Day 1, which has the enormous benefit of the author being present! I'll make a few quick summaries.  The tweets for today can be found in two semi-thematic Storify entries: one gives general coverage and of ONT's demos, whereas the other covers ONT's technical talks and talks by users.

Thursday, December 01, 2016

Oxford Nanopore New York City Meeting, Day 1

Oxford Nanopore officially kicked off its Community Meeting in New York City today; a training session took place yesterday.  Already there have been several interesting announcements and presentations, including a new prototype sample prep gadget, a new basecaller which improves homopolymer calling, a read-both-strands approach that isn't 2D sequencing and details on multiple human genomes run on MinION. A reminder: I'm working only from tweets; I'm not at the meeting.