#nanoporeconf — Public Fediverse posts

@nanopore My selected novel statements from ONT's Tech Update from the 2024 Nanopore Community meeting:

* Updated documentation centre is public: no need to log in

* For large-scale human sequencing (thousands and thousands of individuals), >90% runs over 100 Gb (30X)

* 24-plex direct RNA barcoding kit

* Improved enzyme motor speed, ONT have got a flow cell over 270 Gb yield

#Nanopore #NanoporeConf

@nanopore Should probably get this link out sometime before the conference ends, just in case it interests anyone...

My notes for London Calling 2024:

https://gringer.gitlab.io/presentation-notes/2024/05/22/london-calling-2024/#update-from-oxford-nanopore-technologies

#NanoporeConf

How can we teach data literacy skills and plant genomics to students? Katharina is sharing our experiences through an online poster and on-demand-talk at #LondonCalling2024.
Details are available here: https://doi.org/10.1515/jib-2023-0033
#NanoporeConf #Genomics @PuckerLab

How to teach third generation sequencing and data analysis? Katharina Wolff is going to share the experiences of our "Data Literacy in Genome Research" courses at #LC2024
https://doi.org/10.1515/jib-2023-0033
#nanoporeconf #Genomics #londoncalling @PuckerLab

Interested in the genomic secrets of medicinal plants? Ronja Friedhoff is going to present many of our genome sequencing projects at #LC2024 including Digitalis and Urtica
https://doi.org/10.1101/2024.02.14.580303
#nanoporeconf #Genomics #londoncalling @PuckerLab

#NanoporeConf @[email protected] I think @[email protected] is selling themselves short with regards to number of genomes per PromethION flow cell. With 15kb reads, the coverage required to hit every base is about 10X.

With 650bp reads, the required coverage is about 15X.

What I'm saying is that because of longer reads, ONT doesn't need to do 40X for a human genome. They're already at 3 genomes per flow cell with 150 Gb output.

https://www.reddit.com/r/genomics/comments/z2sj1q/comment/ixj1rgg/?context=3

One thing I haven't checked about #NanoporeConf is whether the on-demand recordings also record question time this year. This has not been the case for what @nanopore has done in previous years, and I find that the question sessions add an interesting sprinkle of flavour to presentations, so talks feel a bit incomplete without them.

#NanoporeConf @nanopore it was great to hear Kimberley Billingsley give specific detail about megaruptor settings from the wet-lab protocol, after a high-level talk about a big project around AD through the CARD long-read sequencing initiative.

@nanopore #NanoporeConf timelines [from Rosemary Dokos' summary]:

* Now - MinKNOW 23.04 with pod5 & 5kHz basecalling
* June - High-duplex EA; rapid PCR barcoding Kit14; Dorado basecalling speedup
* July - RNA04 developer access; multiplex ligation kit
* August - Cas9 multiplex kit14; MinION Mk1D developer
* September - cDNA sequencing kit14
* October - P2i EA; cyclomics EA
* November - TurBOT developer, 384-barcode native barcoding
* December - iPad case developer, 16S kit V14

@nanopore #NanoporeConf ... [continued]

highlights from the technology talk:

* SmidgION ASIC (400 channels, no MUX low power consumption) working; getting q20+ as well as duplex
* MinION MkII - cheap; 5-10 Gb per flow cell
* Grongle - 8x MkII flow cells sequencing in parallel
* New MinION ASIC coming; will be swapped out for existing MinION flow cells
* VolTRAX / TraxION upgrade - reagents included in pack; integrated with sequencer; just drop sample in

@nanopore #NanoporeConf my highlights from the technology talk:

* Duplex rates up to 85-90% (over 50Gb native; over 100 Gb duplex when using PCR)
* Changing to 5 kHz sampling model; getting 99% accuracy SUP, 99.5% accuracy HAC
* RNA04, 2x faster motor, really boosted accuracy to 95%
* Changing flow cell buffers on the trans side, 50% boost to throughput

... [to be continued]

As I predicted, #nanoporeconf dragged me back onto Twitter!

Final talk of #nanoporeconf #NCM2022 I chuckled a little

Hello #NanoporeConf! Join me at 15:35 EST (20:35 GMT) for an online bioinformatics speakeasy. We'll chat in hushed tones over cocktails (BYOB) about #nanopore bioinformatics. Stop by and ask me about our recent EPI2ME Labs release! Access through the app, password is applepore...

The Mantas Sereika talk on microbial genome from metagenomes was intriguing, that's for sure. Never knew about cable bacteria - wish I had more time and ask better thought out questions. #nanoporeconf #ncm2022

Exciting #nanopore updates for RNA biologists announced last night. FINALLY some new chemistry development for direct RNAseq & base caller model updates to go with! ONT's developed many bespoke helicases via an ML-guided engineering effort in 2022, and we're getting one for RNA. Supposedly faster & more consistent motor speeds, improved RNA base calling with accuracy up to 96%, and 3X output improvements from the chemistry changes. All coming next year, early access in Q1.
#NCM2022 #NanoporeConf

One personally curious note at #NCM2022 #nanoporeconf - where are all the field evolutionary biologists, and longer-term reports based on sequencing and analysis? Or have I just missed them - I know there are work being done.

My first NCM experience had been fascinating so far - I can definitely imagine NCM format being an absolutely brilliant move on ONT's part in both addressing research community needs & perhaps shaping at least some of the discussions and interest. Latter via looking at young, emerging researchers I think, so I'd consider this a win-win scenario. #nanoporeconf #ncm2022

Time to mentally prepare for whatever is coming in the tech update. Place your bets! #Nanoporeconf

As with previous years, I will be doing a bit of note taking for #NanoporeConf. This will at least include technology updates from @nanopore, but also whatever other presentations tickle my fancy.

https://gringer.gitlab.io/presentation-notes/2022/12/06/nanopore-community-meeting-2022/

Nanopore-only phasing #nanoporeconf

Karen Miga keen to get T2T assemblies with one device, it's on her Christmas wishlist. #nanoporeconf

Major FOMOs about #NanoporeConf NCM, first one in 7 years I can't attend, will have to make do with the odd talk here and there (thanks @[email protected] for making it hybrid!)
Here's a couple pics from the first NCM at @[email protected] in 2015 for the nostalgics

This sign has helpfully reminded me what time my talk is #nanoporeconf

An actual justification for the fish choice 😂 #nanoporeconf

@vellamike Dorado to be added to Minknow in the next few months #nanoporeconf