H/t to Nava for spotting this & posting to ASeq discord First question posted to @nanopore CEO Gordon Sanghera at #JPM25 had 2 parts: 1. Do they have long read technology? 2. Do they see value in long reads? - ThreadSky

omicsomics.bsky.social • 46 days ago

H/t to Nava for spotting this & posting to ASeq discord

First question posted to @nanopore CEO Gordon Sanghera at #JPM25 had 2 parts:

1. Do they have long read technology?
2. Do they see value in long reads?

Comments

tgtcatcgtatttct.bsky.social•45 days ago

It was a real missed opportunity that every question after wasn't about when did they start offering long reads. See how long until he thought he was in a simulation

iansudbery.bsky.social•45 days ago

I had to read this everyday times to make sure I wasn't misunderstanding something.

iansudbery.bsky.social•45 days ago

Man, the lack of editing here is annoying.

Several times. I had to read it several times (but clearly didn't read my post several times)

timtriche.bsky.social•45 days ago

I preferred the original

I laughed everyday times

omicsomics.bsky.social•46 days ago

Gordon of course was a pro, but I can imagine a stream of ancient Anglo-Saxon vocabulary being barely held back

omicsomics.bsky.social•46 days ago

If any LLM can be less of an embarrassment in your job, you should bail

phil100.bsky.social•45 days ago

From memory Gordon took the first question about long reads in good spirit. He discussed the current limits of short and long reads and added words to the effect of there was no reason why a full chromosome could not be read in one read soon

gringene.org•45 days ago

There are a few reasons. Here are some:

1. The sequencing wells on MinION flow cells are 100μm across, which is about 300kb, and those edges are quite sharp.

2. The simple act of pipetting is likely to shear DNA.

3. 10 Mb at 500b/s is ~5.5 hours. The MUX scan frequency is less than this.

gringene.org•45 days ago

Why couldn't a full chromosome be sequenced (which I'm assuming is at least 10 Mb)?

Likelihoods that increase with length:

4. Presence of a single-stranded break.

5. Presence of complex secondary structures (e.g. G-quadruplex).

6. Reads jamming and knotting in the pores.

phil100.bsky.social•45 days ago

Hi David, I can't remember the precise wording used by Gordon, of type of hardware being discussed, if any, but I will revisit the audio and update the post if there is more info. He suggested some ultra long reads have already been achieved, up to 3.5m bases. Probably PromethION?

gringene.org•45 days ago

Yes, I'm aware that multi-megabase reads have been sequenced, first by the community, then by ONT. I think there has also been a single-read sequence of a small yeast chromosome, which is why I'm explicitly specifying >10 Mb.

All I'm saying is that there are reasons why sequencing is difficult.

gringene.org•45 days ago

Yes, my memory was correct; a yeast chromosome has indeed already been sequenced telomere-to-telomere:

https://twitter.com/vellamike/status/1793330011363008607

omicsomics.bsky.social•45 days ago

They claim 4 different ones downthread

gringene.org•45 days ago

In other words, there are reasons why a full chromosome could not be read in one read *soon*.

Not impossible (unless intact full-length chromosomes just don't exist), but there are a number of physical and software-based challenges that need to be fixed first.

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