My enthusiasm for nanopore sequencing is well known; we have some awesome software for working with the data; we won a grant to support this work; and we successfully assembled a tricky bacterial genome. This all led to Nick and I writing an editorial for Nature Methods.
So, clearly some bias towards ONT from me.
Having said all of that, when PacBio announced the Sequel, I was genuinely excited. Why? Well, revolutionary and wonderful as the MinION was at the time, we were getting ~100Mb runs. Amazing technology, mobile sequencer, tri-corder, just incredible engineering – but 100Mb was never going to change the world. Some uses, yes; but for other uses we need more data. Enter Sequel.
However, it turns out Sequel isn’t really delivering on promises. Rather than 10Gb runs, folk are getting between 3 and 5Gb from the Sequel:
— John Kenny (@jgskenny) December 8, 2016
At the same time, MinION has been coming along great guns:
Yesterday we announced 5-10Gb, high accuracy MinION Flow Cell release, PromethION Early Access, more. Missed it? https://t.co/8GTto8W9Ur
— Oxford Nanopore (@nanopore) September 30, 2016
Whilst we are right to be skeptical about ONT’s claims about their own sequencer, other people who use the MinION have backed up these claims and say they regularly get figures similar to this. If you don’t believe me, go get some of the World’s first Nanopore human data here.
PacBio also released some data for Sequel here.
So how do they stack up against one another? I won’t deal with accuracy here, but we can look at #reads, read length and throughput.
To be clear, we are comparing “rel2-nanopore-wgs-216722908-FAB42316.fastq.gz” a fairly middling run from the NA12878 release, m54113_160913_184949.subreads.bam and one of the Sequel SMRT cell datasets released.
Read length histograms:
As you can see, the longer reads are roughly equivalent in length, but MinION has far more reads at shorter read lengths. I know the PacBio samples were size selected on Blue Pippin, but unsure about the MinION data.
The MinION dataset includes 466,325 reads, over twice as many as the Sequel dataset at 208,573 reads.
In terms of throughput, MinION again came out on top, with 2.4Gbases of data compared to just 2Gbases for the Sequel.
We can limit to reads >1000bp, and see a bit more detail:
- The MinION data has 326,466 reads greater than 1000bp summing to 2.37Gb.
- The Sequel data has 192,718 reads greater than 1000bp, summing to 2Gb.
Finally, for reads over 10,000bp:
- The MinION data has 84,803 reads greater than 10000bp summing to 1.36Gb.
- The Sequel data has 83,771 reads greater than 10000bp, summing to 1.48Gb.
These are very interesting stats!
This is pretty bad news for PacBio. If you add in the low cost of entry for MinION, and the £300k cost of the Sequel, the fact that MinION is performing as well as, if not better, than Sequel is incredible. Both machines have a long way to go – PacBio will point to their roadmap, with longer reads scheduled and improvements in chemistry and flowcells. In response, ONT will point to the incredible development path of MinION, increased sequencing speeds and bigger flowcells. And then there is PromethION.
So is the war already over? Not quite yet. But PacBio are fighting for their lives.