When will nanopore sequencing push short-reads (i.e. Illumina) off their pedestal? According to Clive PromethION is the Illumina killer…but this same conversation was going on many times at London Calling. I wanted to highlight two areas that might be about to flip to ONTs advantage (one of which I’m really excited about).


With costs dropping precipitously on MinION (if you can get 10GB+) and PromethION on the way for the end of this year as a real production machine it looks like the sensible choice for a high-quality genome would be Nanopore + Illumina, but given a little more improvement genomes might be best done “nanopore only” very soon?

My lab does not sequence many genomes but when the next 1000 genome project comes along I guess I should pick up the phone and talk to Clive as well as Franics?


Lets be absolutely clear, until ONT’s Direct RNA-Seq was launched (see most recent BioRxiv submission from Andrew Smith et al) pretty much nobody was actually sequencing RNA! However there were talks about 10 million+ 1D cDNA reads from the new protocols being developed by Dan Turners applications group at ONT.

My lab does a LOT of RNA-Seq, primarily for DGE and mainly using single-end 50bp reads (feel free to comment Mick). We aim for 10-20 million per sample.

Assuming a 1000bp ONT cDNA read equates to 20 Illumina SE50 reads (something we should debate) then those 10 million ONT cDNA reads might allow me to sequence 20 samples (at 1000bp average read length) or 40 (at 2000bp) on a single MinION flowcell. I’ve not really pushed higher than 2000bp as the number of Human transcripts longer than this is probably less than 50%.

I’ve also held off debating 1) the additional benefits of counting isoforms directly, and 2) of the impact direct RNA-Seq will have on biological analysis.

Food for thought…see you in Gordon’s “good morning” rock family trees intro.

Let me know what you think will be the first application “lost” by short-read technologies?