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I'd suggest the title be "...speed of nanopore DNA sequencers" as this tech doesn't apply to the majority of sequencers. (Not to say it's not exciting: I find nanopore sequencing to be the most exciting thing in the field)
Earlier quoted context omitted.
Can it be used instead of PCR Covid test for example?
This would be me more applicable to looking for variants of a known gene. For example, measuring mutation rates within known covid-positive samples.
I'd suggest the title be "...speed of nanopore DNA sequencers" as this tech doesn't apply to the majority of sequencers. (Not to say it's not exciting: I find nanopore sequencing to be the most exciting thing in the field)
to me nanopore seq is not that promising. it has been here for a long time now and the benefits didn't convince a lot of customers to adopt it. there are 2 main use cases now in precision medicine: rare disease and cancer. for both you need high precision reads, which nanopore doesn't provide.
I'd suggest the title be "...speed of nanopore DNA sequencers" as this tech doesn't apply to the majority of sequencers. (Not to say it's not exciting: I find nanopore sequencing to be the most exciting thing in the field)
to me nanopore seq is not that promising. it has been here for a long time now and the benefits didn't convince a lot of customers to adopt it. there are 2 main use cases now in precision medicine: rare disease and cancer. for both you need high precision reads, which nanopore doesn't provide.
On the bacterial side, it is fantastic for quickly sequcinging and closing genomes. Personally, I think the killer use case is field portable and real time sequencing of pathogens. I've worked with groups (.gov and private, defense and health related) that want to put minION + flongles to use in applications like early detection for bio terrorism and pathogen surveillance.
Earlier quoted context omitted.
theyre not really similar problem, genome assembly is a problem that is most effectively solved in the lab and with traditional graph algorithms. protein folding fits very nicely into structured prediction and has a very quantitative way of measuring performance. Genome assembly is more qualitative, to say the least. given a bunch of reads of short(50-300bp) or long (1000-100,000 bp) lengths (we use different algorit…
No practical assemblers take assembly as a Hamiltonian problem.
Earlier quoted context omitted.
This would be me more applicable to looking for variants of a known gene. For example, measuring mutation rates within known covid-positive samples.
Nanopore isn’t great for looking at generic mutation rates (many will be single nucleotide polymorphisms) due to the high error rate. It’s much better at looking for splicing patterns and epigenetic modifications. Splicing patterns could conceivably change due to mutation, but that’d be a pretty dramatic mutation.
Earlier quoted context omitted.
No practical assemblers take assembly as a Hamiltonian problem.
many long read assemblers (good ones, at that) treat it as a hamiltonian problem.
Michael Schatz has been involved in a number of interesting computational biology projects. I worked in a bioinformatics lab ~10-12 years ago and I remember using his fast short read aligner to help speed things up. Back then the nanopore devices were still just rumors. Computers have Moore's law with a base or time constant of 12-24mo. Batteries seem to have the same with a base of about 10 years (slow Moore's law I…
https://www.nature.com/news/technology-the-1-000-genome-1.14...
Michael Schatz has been involved in a number of interesting computational biology projects. I worked in a bioinformatics lab ~10-12 years ago and I remember using his fast short read aligner to help speed things up. Back then the nanopore devices were still just rumors. Computers have Moore's law with a base or time constant of 12-24mo. Batteries seem to have the same with a base of about 10 years (slow Moore's law I…
The cost of sequencing is dropping much faster than Moore's law. https://www.nature.com/news/technology-the-1-000-genome-1.14...
"For longer targets such as chromosomes, common approaches consist of cutting (with restriction enzymes) or shearing (with mechanical forces) large DNA fragments into shorter DNA fragments. The fragmented DNA may then be cloned into a DNA vector and amplified in a bacterial host such as Escherichia coli. "
Two questions:
1) OK, we cut up the DNA and replicate it. How in the heck do we assemble the pieces together to restore the original ordering? I've got three pieces A,B,C. How do I know it was originally ABC or CBA or BAC etc? I can correctly sequence a piece ... but what I want is the sequence of all base-pairs in their original order. How on earth do they do that?
2) DNA spends most of its time wrapped up around histones. How do does one get it off the histones for access to sequencing?
3) Less interesting: unless we sequence the whole chromosome researches must pick off a piece ... how do we know which piece to pick off and how do we know where it's crammed around the histones?