More do it at home @nanoporetech.com sequencing is being announced on X (x.com/SethSHowes/s...)
A blog post by Seth Howes (iwantosequencemygenomeathome.com). Hope London Calling will feature a tinkerer session this year.
2 cents will not buy you useful amounts of data yet 😉
There's a reason why most undiscovered taxa come from soils, sediments, wetlands, etc: www.nature.com/articles/s41...
The way I prefer to think about it is to put that money into long reads and get usable data.
For soil and sediment we do one sample per flowcell. The complexity of these sample types is fairly high for simpler communities barcoding is a good option.
A major milestone for biodiversity genomics: EBP-affiliated projects have now contributed over 6,000 genome assemblies toward the goal of sequencing all known eukaryotic life. 🧬
Thank you to all EBP-affiliated projects behind this work, from sampling and DNA extraction to sequencing and assembly.
Yeah with the powermax you get enough to afford doing the pre prep cleanups + the LSK114 goes well even with low amounts of dna loaded onto the flowcell. Think we maxed out pore occupancy down to roughly 20 ng loaded.
Quite a few flowcells going beyond 200 gbp
Our samples include sediment, soil, sand etc. Power max kit + SPRI cleanup before the LSK prep.
We have received 200+ on several flowcells. Think the record was 260 gbp (estimated).
Our median nanopore yield is around 170 gbp. We see flowcells going beyond 200 gbp quite often.
Our ECE-host framework doesn't care which sequencing platform you use—it’s ready to go once you have mod calling results. The kicker is that we need scalable mod calling from metagenomics. If it doesn't scale, the ECE-host analysis can't happen.
Congratulations @wshuai.bsky.social and co-authors!
We’re excited to introduce MODIFI, our new scalable method for detecting DNA modifications in PacBio metagenomic data and estimating ECE-host linkage.
Check out the preprint: www.biorxiv.org/content/10.6...
Demand for ai generated cat videos etc 📈
Will be even more by Monday 🤣 Our IT team told us that now is a bad time to buy hardware... Orders already placed get cancelled due to price hikes or delivery issues. I fear that we are just seeing the beginning and now will turn out to have been a bargain a year from now 🤣
videocardz.com/newz/hp-unve... wow, 4 Nvidia RTX Pro 6000 Blackwell GPU support. Future Oxford Nanopore attachment for the P48 sequence? @kirk3gaard.bsky.social
_720 Gbp_ marine nanopore metagenome -> 328 circular prokaryotic contigs: using myloasm!
Insane work by Lui and Nielsen. Also shows how modern long read assemblies can disentangle coexisting strains and reveal ecological insights.
Will 2026 be the year we finally see something new from @nanoporetech.com or are we stuck due to the clinical focus? Next generation ASIC chips would be the opportunity to align product lines. One flowcell to rule them all?
A new era for #ONT amplicon sequencing?
We show that #ONT #amplicon sequencing now achieves accuracy sufficient for #ASV resolution using standard Illumina-based pipelines. We validated this by sequencing identical amplicons on #ONT and #PacBio. @nanoporetech.com www.biorxiv.org/content/10.6...
The sun brings out the green @nanoporetech.com 🟩🟩🟩🟩🟩🚀🧬
Happy Friday everyone.
It is absolutely outrageous that Moderna’s flu vaccine was met with a “refusal-to-file” even after their approved their protocol with FDA and carried out the trial as agreed. This vaccine works better in older adults than the current flu vaccines.
apnews.com/article/mode...
Hey @bsky.app can we get a poll option?
claude: I have no idea why we now have more unmapped reads than before after adding in mismatch scoring
me: did you reverse complement the genome sequence?
claude: i'm a dumbass
New hifiasm-ONT assembly method delivers high-quality, cost-efficient near T2T assemblies using standard Oxford Nanopore Simplex reads, broadening access to comprehensive genome assemblies across research and clinical applications. https://bit.ly/4awzU15
En anden ting er effektiviteten af bilen. Hvor mange km/min tilføjer man 😁⚡🚗
When you look up something and all the links are already purple 😉
I think Single-M was written with that use-case in mind. Haven't tested it personally so can't vouch for it, but likely worth a try.
www.nature.com/articles/s41...
Well we still mostly run denovo assembly of everything. But people like sylph for speedy classification of reads github.com/bluenote-157...
Which assembler do you use?
alignment of reads to reference genome. a poly-t region was created by a single read in the dataset.
interesting nanopore sequencing experience. found this in the middle of my genome assembly. driven by a single read with a big homopolymer in the middle of it? pretty weird, something to look out for i guess (i wonder how many of these are in Genbank...)
