Oxford Nanopore Doesn't Disappoint

Oxford Nanopore's AGBT presentation should have just finished up, so the embargo is off.  Oxford was kind enough to chat with me last night and to share their press release in advance; on the call were CTO Clive Brown, SAB member Ewan Birney and Director of Communications Zoe McDougall.  A real challenge posed by Oxford's news is trying to write about it without slipping into clichéd techspeak about what they will be releasing later this year ("second half").

2012: Enter the Nanopores?

This summer will make it twenty years since I first heard of the concept of nanopore sequencing.  A very affable post-doc in George Church's lab was starting some experiments in the concept.  Unbeknownst to any of us, another group at Harvard in the Biolabs (Dan Branton's) was also working on a nanopore sequencing technology.  In the time since then, the field has generated many papers and much speculation, but no workable sequencer.  I had started joking a few years ago that nanopores were the monorails of sequencing: always the technology of the future.  To be a bit more fair, nanopores had started to resemble nuclear fusion, a tantalizing vision always just out of technological reach.

Does Illlmina Also Have A Homopolymer Problem?

One of the most widely-publicized error modes with Ion Torrent and 454 sequencing has been the challenge of correctly counting the number of bases in homopolymer runs.  Because these chemistries use non-terminating nucleotides, polymerase is free to add as many as possible.  Unfortunately, the signal linearity breaks down, making it difficult to correctly count.  Ion Torrent today released a note on homopolymers, but rather than plowing this well-trod ground it goes for a less publicized problem: Illumina having a more specific challenge in this department.  The note is available on the Ion Community, free registration required.

Roche Guns For Illumina

Due to a business dinner & general exhaustion, I turned in early last night & was caught unaware this morning of the big news: Roche is making a hostile takeover bid for Illumina.  Ugh!

Sequencing Technology Fireworks

I actually awoke today expecting an exciting press release, but I sure wasn't prepared for the big announcements from Ion and Illumina.  Not that they were totally unexpected, but there's a huge difference between speculation and announced products (which, of course, are hugely different from ones you can actually buy!)

Ion Torrent Pairs: To What End?

Ion Torrent quietly released a set of paired end datasets over the holiday break.  This is a bit embarassing for me, as in my last post on Ion I stated the platform "will probably never have paired ends" and in fact Ion had already announced the protocol.  Oy!  I also missed their mate pair protocol being released, though the document itself is another victim of Ion's incredibly counterproductive security policy.  If you don't own a PGM, you can't access the document -- never mind if you are trying to plan for a potential buy or are preparing a library for a friend/collaborator to run.  

Year's End

I hoped this year to push myself to blog more frequently and regularly.  Clearly I did better than some years, but not up to the standard I had hoped for.  I've also realized that I missed noting some significant personal milestones.