#NanoporeConf @nanopore@a.gup.pe I think @nanopore@bird.makeup 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

#NanoporeConf @joepdl started his talk on targeted sequencing of infectious diseases with a mihi, then a content warning for COVID, then a "results may differ depending on your government" disclaimer.

Great to see a little bit of fatalistic humour to brighten my day!

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.

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]

#NanoporeConf red eye time. I'm up after a few hours of sleep for the technology update part of @nanopore London Calling. I've set up my computer to auto-push my notes every five minutes, and the result will appear here:

https://gringer.gitlab.io/presentation-notes/2023/05/18/london-calling-2023/

Just noticed @joepdl in the #NanoporeConf auditorium audience shot!

@nanopore #NanoporeConf not liking the COVID pandemic past tense language. Not seeing many (if any) masks in the audience. I was under the impression that infection levels were fairly high in the UK.

@nanopore #NanoporeConf #ECRSpotlight Kalinka Sand Knudsen will be talking about fantastic methanotrophs; using raw nanopore reads, then converting to protein sequences, the sequences are only as good as Illumina short reads. She has found a way to do better.

#ShotsFired

RT nanopore: Now on stage, our first speaker NCM 2022, \@khmiga (KM) with her talk: Expanding studies of global genomic diversity with complete, telomere-to-telomere assembly of diploid genomes. #nanoporeconf

https://twitter.com/AdrienLeger2/status/1600132522624417792

@AdrienLeger2: We are getting pretty good at 5hmC calling with @nanopore !
#NanoporeConf @Stoibs11 https://t.co/yARrfyd1Lz https://t.co/GDFuea7mX1

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

RT @ChristosArgyrop@twitter.com

Amazing talk by Sean Wang from the Minnesota Dpt of Health about #SARSCOV2 genomic sequencing at the Panel Plenary in the #Nanoporeconf.

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