The ever-declining costs of DNA sequencing technologies — no, I’m not going to show that graph — has meant that the field of genome assembly has exploded over the last decade.
Plummeting costs are obviously not the only reason behind this. The evolving nature of sequencing technologies has meant that this year has pushed us into the brave new era of megabase pair read lengths!
Think of the poor budding yeast: the first eukaryotic species to have its (12 Mbp) genome sequenced. There was a time when the sequencing of individual yeast chromosomes would merit their own Nature publication! Now only chromosome IV remains as the last yeast chromosome whose length couldn’t be exceeded by a single Oxford Nanopore read (but probably not for much longer!). Update 2018-09-12: a 2.2 Mbp Nanopore read means that chromsome IV's length has now been eclipsed!
Looking for genome assembly publications
I turned to the font of all (academic) knowledge, Google Scholar, for answers. I wanted to know whether interest in genome assembly had reached a peak, and by ‘interest’ I mean publications or patents that specifically mention either ‘genome assembly’ or ‘de novo assembly’.
Some obvious caveats:
- Google Scholar is not a perfect source of publications: some papers are missing, some appear multiple times, and occasionally some are associated with the wrong year.
- Publications are increasing in many fields due to more scientists being around and the inexorable rise of if-you-pay-us-money-and-randomly-hit-keys-on-your-keyboard-we-will-publish-it publishing. So a rise in publications in topic 'X' does not necessarily reflect more interest in that topic.
- Not all publications concerning genome assembly will contain the phrases ‘genome assembly’ or ‘de novo assembly’.
Caveats aside, let’s see what Google thinks about the state of genome assembly:
Does this tell us anything?
So there’s clearly been a pretty explosive growth in publications concerning genome assembly over the last couple of decades. Interestingly, the data from 2017 suggest that the period of exponential growth is starting to slow just a little bit. However, it would seem that we have not reached ‘peak genome assembly’ just yet.
There are, no doubt, countless hundreds (thousands?) of publications that concern technical aspects of genome assembly which have reached dead ends or which have become obsolete (pipelines for your ABI SOLiD data?).
Maybe we are starting to reach an era where the trio of leading technologies (Illumina, Pacific Biosciences, and Oxford Nanopore) are good enough to facilitate — alone, or in combination — easier (or maybe less troublesome) genome assemblies. I’ve previously pointed out how there are more ‘improved’ assemblies being published than ever before.
Maybe the field has finally moved the focus away from ‘how do we do get this to work properly?’ to ‘what shall we assemble next?’. In a follow-up post, I’ll be looking at the rise and fall of different sequencing technologies throughout this era.
Update 2018-08-13: Thanks to Neil Saunders for crunching the numbers in a more rigourous manner and applying a correction for total number of publications published per year. The results are, as he notes, broadly similar.