Tuesday, September 01, 2015

Ion's S5

The Ion Torrent team rolled out a new sequencer line this morning, the S5.  The S5, whose impending release had been tipped on the internet by the leak of a manual, arrives in two models, the standard and the XL, which differ only by on-board computing power and not sequencing metrics.   As has been the trend, Ion's focus is entirely on focused sequencing, and the new lineup emphasizes making targeted sequencing with AmpliSeq and other approaches fast and simple.

Wednesday, August 26, 2015

The Road to Hell is Paved with Bioinformatics Formats

If you really want to raise a bioinformaticist's blood pressure, loudly declare your new tool generates output in brand new data formats.  This leads to the frequent observation that a large fraction of bioinformatics work is simply converting formats. It is probably consensus that the field is awash in too many formats, though it is equally clear that we can't agree on which should survive.  Between some recent news and a Twitter thread on the subject that erupted last night, there was a bunch of fodder for me to collect in a Storify -- and to lay out my own idiosyncratic views.

Monday, August 24, 2015

Do Helix's Numbers Work?

A number of efforts in the consumer genomics space have been attempted in the past, with 23andMe appearing to make limited headway and Knome not much at all.  I haven't been able to get any investment interest in my own concept, though perhaps that's because it was tongue-in-cheek (or tongue held out while panting).  Last week brought a big splash, with a new company Helix launching with $100M and three major players as backers: Illumina, LabCorp and the Mayo Clinic

Friday, July 10, 2015

Clinical Metagenomics Pipelines: Revisiting & Reflecting

When I set out to start this blog nearly over eight years ago, I set myself a number of goals.  One goal was to take some risks -- not crazy risks but to not just play it safe.  But counterbalancing that goal was one to be open, accurate and honest. My piece last week on clinical metagenomics pipelines had a fair amount of attention, and resulted in an ongoing electronic conversation with one of the key parties.  In the course of this, there are now parts of that piece I wish I had handled differently. Some other important topics have been raised, and I would like to cover here.

Thursday, July 02, 2015

Leaky clinical metagenomics pipelines are a very serious issue

Update: Some significant issues with the tone of this post are discussed in a follow-up.

I am a firm believer that the practice of science is the result of contingency; we do not necessarily have the best scientific culture possible but rather one which has evolved over time driven by chance, necessity and human nature.  We should never hesitate to re-examine the way science is actually practiced, and that particularly holds true for how we analyze data and publish results.  A re-analysis of a prominent Lancet paper has just come out in F1000, and this work by Steven Salzberg and colleagues illustrates a number of significant issues that slipped past the conventional peer review publishing practice

Tuesday, June 30, 2015

June 2015: Busting Out All Over with Genomics Technology

This month I again entered the prime of my life, though next year my programming brother points out that next year I (and the first Apollo manned missions) hit the big 30.  Beyond my personal milestone, it's been a busy last couple of weeks on the genomics technology front. Despite a lack of conferences or other traditional venues, big news has poured out from Pacific Biosciences, BioNano Genomics, Genapsys, BGI (which had another announcement earlier in the month), 10X Genomics and a pair from Oxford Nanopore.

Monday, June 08, 2015

BGI Unveils a Sequencing Factory to Go

When I was in George Church's lab, he submitted a grant proposal (which, alas, was not funded) for a sequencing factory to generate one megabase of data per day.  In those days that was an ambitious goal, and the plan would have truly been on a factory scale, with a large workforce and an assembly line of stages to yield the final product of data.