Illumina vs Oxford Nanopore | Long-read hacking?

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Күн бұрын

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@davidhoudek9083 Жыл бұрын

As always, very interesting. And above all: Thank you! :-D Can I ask you a few questions? Who are the long read customers and who are the short read customers? Or when do you use what? If long reads are so cheap, why doesn't everyone move to long reads in the future? And you talk about "all these new technologies". What else is worth mentioning? And what about Pacific Biosciences? At the same stage/level as Oxford Nanopore? Perhaps you could touch on some of this in your next videos. Greetings from Germany 🙂

@bad.genome Жыл бұрын

Thanks so much asking and great questions, sorry I didn't cover them in this video! Long reads are used to detect changes in DNA that occur over larger regions or for analysing entirely new DNA sequences (hence we might not have a "reference" to compare it to). Because it covers a larger region, they are more complex to analyse as well, so it's partly a question of knowing what to do with the data plus they require more computational power to analyse. Long reads are "cheaper" in a relatively sense that for Nanopore specifically, it is possible to get started with just the basic kit (called the Minion) without having to purchase a big sequencer to get started, having said that, there is still a bit of work need to "prepare" the DNA sample before feeding it into the the sequencer. The small form factor has meant it's been possible to set up multiple labs in Indonesia during COVID (rather than ship them to a central lab), also they've run Nanopore sequencing in space, and rapidly set up Nanopore to sequence Ebola. I have to confess my knowledge of PacBio is a bit dated and I need to beef up my reading on this. But I am planning to do a comparison between the different long read technologies. It's just that I've had more contact with Nanopore these years, but this is a great prompt for me to look further outside my expertise. Thanks for the great feedback!

@ciaranbrowning6226 3 ай бұрын

@@bad.genome to tag onto BG's response. My background is not necessarily genomics, its techniques or analysis - rather its application, as such my background is haematology. My thought would be not to divide this between who would be LR and SR customers, rather, why would the current body of application jump from SR to LR? Why would I encourage my genomics lab to jump to or have access to this in a practical sense? For example, what about a fixed of key recurrent mutations in AML, when I want (at and the need to provide and ), in a regular routine manner (, and clonality of the course of management, what about subclones), for without necessarily the workload, analytic demand, and expertise needed in SR technology, and the need for such high accuracy. Oxford MinION has an application paper in AML targetted sequencing, have also announced PromethiION which technically could run up to 24 sequences simultaneously (If I understood that correctly), and are ambitious to promote their aim to enable 'all context modification sequencing' - the ability to sequence in any context.

@karthikrajah8680 9 ай бұрын

This is so well explained! Completely fanboying over this video

@blu3_enjoy Жыл бұрын

Great insight and overview as always. Thanks. You're a really good speaker

@fishonbicycle 6 ай бұрын

you sir is a great communicator. thank you!

@MrKwontastic 2 ай бұрын

Can you do a video on how to do a simple nanopore sequence using the Min-ion?

@dr.zakuanazizishamsulharum3280 3 ай бұрын

Thank you sir for this well explained video.

@andresando 6 ай бұрын

Where is the Oxford Nanopore video?

@luciususiholo6956 Жыл бұрын

What’s the difference between long read and short read sequencing and what advantages does one have over the other

@bad.genome Жыл бұрын

Great question! It's how many DNA letters in a row the machine can read at a time. Longer reads are helpful in detecting DNA changes that happen over a large region. They are also great for sequencing DNA that we've never seen before. Having said that, machines that sequence short reads do them at very high resolution (many many short reads) resulting in higher accuracy. So both have their advantages depending on what we're trying to detect. Thanks for asking this.