> But Nanopore sequencing is still far from perfect due to its high error rate. Any clinical sequencing is still done using sequencing by synthesis (at which Illumina has gotten very good over the past decade).
There is no reason for Nanopore to supplant sequencing-by-synthesis for short reads - that's largely solved and getting cheaper all the while.
The future clinical utility will be in medium- and large-scale variation. We don't understand this in the clinical setting nearly as well as we understand SNPs. So Nanopore is being used in the research setting and to diagnose individuals with very rare genetic disorders.
(edit)
> We are not “in the nanopore era of sequencing”. We are (still) firmly in the sequencing by synthesis era.
I also strongly disagree.
SBS is very reliable but it's common (if Toyota is the most popular car, does that mean we're in the Toyota internal combustion era? Or can Waymo still matter despite its small footprint?).
Novelty in sequencing is coming from ML approaches, RNA-DNA analysis, and combining long- and short-read technologies.
I agree with you. Long reads lead to new insights and over time to better diagnoses by providing better understanding of large(r) scale aberrations, and as the tech gets better will be able to do so more easily. But is really not there yet. It’s mostly research and somehow it’s not really improving as much as hoped, I get the feeling.
There is no reason for Nanopore to supplant sequencing-by-synthesis for short reads - that's largely solved and getting cheaper all the while.
The future clinical utility will be in medium- and large-scale variation. We don't understand this in the clinical setting nearly as well as we understand SNPs. So Nanopore is being used in the research setting and to diagnose individuals with very rare genetic disorders.
(edit)
> We are not “in the nanopore era of sequencing”. We are (still) firmly in the sequencing by synthesis era.
I also strongly disagree.
SBS is very reliable but it's common (if Toyota is the most popular car, does that mean we're in the Toyota internal combustion era? Or can Waymo still matter despite its small footprint?).
Novelty in sequencing is coming from ML approaches, RNA-DNA analysis, and combining long- and short-read technologies.