Ahh, have you seen this one? To me, this is the crown jewel of long read metagenomics at the moment? Gives some guidelines on how deep you need to sequence soil to get decent MAG recovery. www.nature.com/articles/s41...

Have not done much @nanoporetech.com sequencing lately but this looks pretty 🟩🟩🟩🟩🟩🟩 #MFDExtreme

Gotta catch em all! A little late night sampling for the MFD Extreme project. What microbes call this sand their home?

Beautiful evening for sampling. Microbes live in so many funky places and I finally got the chance to hunt them in locations that were not wastewater treatment plants 🎉🦠🧬🇩🇰 #MFDExtreme

Slowly it's sinking in 😍 Very excited about my new role as #Assistant #Professor @univie.ac.at @cemess.bsky.social! 🦠👩‍🎓🔬 It's great to be part of this fantastic team of friends and colleagues! 🧪 #Microsky

We have a new 3-year postdoc position in our group at the @hifmb.de to study plasmids and plasmids systems of the marine environment to survey their utility in microbial responses to environmental change. Please see the official job ad here, and spread the word: jobs.awi.de/Vacancies/20...

Can we please get Dorado 1.0.0+ in @nanoporetech.com minknow ASAP? 4090 also jumps quite a bit and is getting closer to support a full P2S with live sup 🎉

Got a chance to take the @nanoporetech.com hyp(er accuracy) model for a spin. Pretty decent improvement in read quality 🚀 but expect to spend quite some more GPU hours 😉 (Reads were mapped with minimap2 and identity scores from nanoplot were used for phred score calculations)

With all that is happening it is very exciting to see the Price Lab's very first, in-house, Oxford Nanopore direct RNA seq running! Not bad for a ~3 year expired flow cell!

Wandering while wondering if this sample cup will hold a story exciting enough for @isme-microbes.bsky.social conference in New Zealand next year 🦠

I tested myloasm on a 50x Klebsiella isolate, and it was very fast - only took about 1 minute to complete (on my Macbook).

Promising toolkit for binning and visualizing assembly graphs. The assembly graph is an underutilized source of binning information IMO gbintk.readthedocs.io/en/latest/

It seems we can assemble (reasonably simple populations) of co-existing strains with ONT data now. We assembled 6 single-contig Prevotella copri genomes of > 97% ANI for one metagenome. 4 of them were circular. (The largest metaFlye P. copri contig was 13.4% complete)

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

Most of the remaining errors are homopolymer-length errors, e.g. the genome had G×11 but the assembly had G×10. The rest are mostly 1-bp substitutions and indels. Often these occur at similar motifs within a genome.

New blog post! In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup. Check it out for the full results: rrwick.github.io/2025/05/27/d...

Short-read metagenomic sequencing cannot recover genomes from many abundant marine prokaryotes due to high strain heterogeneity and platform-inherent GC bias (likely viruses, too), but Nanopore long reads can address this. A results thread on our recent preprint 🧵.

In addition to anti-GC and strain bias, certain taxa show systematically underestimated completeness via CheckM1 and 2, so historically much more likely to get erroneously thrown away in fragmented Illumina MAGs—a third reason for the existence of Ghost Taxa. A sub-sub-thread 🧵.

ARTIC 2 is here!

Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.biorxiv.org/content/10.1...

Come join us in Vienna september 8-11 for a great conference on all things microbial Nitrogen cycle abstract deadline is June 15th!

The human pangenome continues to grow and improve! Release 2 is here! Click through for the details, but this is a pretty amazing dataset including not just the phased assemblies, but PacBio HiFi, ONT Ultralong, Dovetail/Illumina Hi-C, PacBio Kinnex, and Illumina WGS for all samples

"they only exist in computers so far" 🤣🤣🤣 I do not trust microbes exist unless I can see them without a microscope 🤣🤣🤣

Here's another comparison for you: "On average, 36.4% of reads mapped back assemblies, and for some samples this mapping was as high as 64.7%" from www.nature.com/articles/s41... (range for all samples in Table S1)

What percent reads mapped to MAGs is "good" for soil or sediment samples? is lower than water samples OK/expected due to more complex communities? 🙏 🖥️🧬 microbiome, metagenomics

Genomes from long-read metagenomic assemblies contain rampant errors, highlighting the pressing need for stricter evaluation methods in long-read assembly algorithms. Read more in our paper with the Eren group. @floriantrigodet.bsky.social @merenbey.bsky.social

Looking for a PhD course about @nanoporetech.com sequencing and metagenomics? Or just an excuse to visit Aalborg (phd.moodle.aau.dk/course/index...)

Before you head off for Easter break, go and register for Genome Science 2025 9th-11th July hosted in Newcastle by the formidable @4130chromo.bsky.social - we’ve got an amazing roster of speakers from academia and all the big sequencing companies - more details at www.genomescience.org.uk/speakers

Considering an apple gpu for your @nanoporetech.com basecalling? Then I hope you have lots of patience or is happy with "fast" mode data quality. github.com/Kirk3gaard/2...

Already some nice entries added to the list for @nanoporetech.com basecalling 🎉 Do you have some nvidia GPUs that are missing?

CoverM is published! CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs

Help your fellow researchers decide what nvidia GPU to buy for their @nanoporetech.com basecalling needs. github.com/Kirk3gaard/2...

Now with pod5s in @enasequence.bsky.social

Okay. So I have not done the @nanoporetech.com native barcoding preps for some years. It went form including an ampure cleanup step and take forward 75 % of your DNA to no ("optional") cleanup and take forward 0.75/15ul=5 % of your DNA. Any inputs on whether yield performance is similar?

Anyone with access to ManusAI, AnthropicAI computer use or openAI operator that have tested it for data uploads to @enasequence.bsky.social or NCBI?

After reading recent blog posts by @omicsomics.bsky.social with the development and history of DNA seq I realized that I was missing an updated figure to summarize it in the style originally by @lexnederbragt.bsky.social (flxlexblog.wordpress.com/2016/07/08/d...) Anyone doing a 2025 edition?

Less than two months to @nanoporetech.com London calling. Anyone secretly testing new pores? Kit chemistry? Devices?

Anyone has been lucky enough to get their hands on some nvidia RTX50XX GPUs and can report basecalling performance with @nanoporetech.com dorado 0.9.1 sup? (5080 here: github.com/nanoporetech...)

There is a silly amount of @nanoporetech.com from the @zymoresearch.bsky.social fecal sample. 1 Well performing PromethION flowcell ;)

A pie graph worth keeping in mind as the NIH budget plummets jamanetwork.com/journals/jam... for 356 new FDA drugs approved

Want @nanoporetech.com data for benchmarking microbe related stuff? Check our data for pure cultures, @zymoresearch.bsky.social mocks and metagenomes ( github.com/Kirk3gaard/M...). Basecalled reads with methylation is in @enasequence.bsky.social . Eventually the pod5s might go there as well.

Anyone has encountered out of memory errors with the P2S running the latest minknow version?

Value of DNA sequencing companies dropping faster than the price per genome?

Did bulk options beyond 32 flowcells magically disappear @nanoporetech.com ?

Looking forward to see how much faster the nvidia RTX5090s will be at basecalling @nanoporetech.com data. Here SUP v5.0.0 with dorado 0.9.1 and the cards that we have available.

Our mSCAPE project has been formally announced to the world by @smhopkins.bsky.social at #FOG2025 today: www.gov.uk/government/n... - a really exciting academic-public health collaboration to build a surveillance platform leveraging NHS metagenomic diagnostic data. @meerac.bsky.social

Recovery of highly contiguous genomes from complex terrestrial habitats reveals over 15,000 novel prokaryotic species and expands characterization of soil and sediment microbial communities https://www.biorxiv.org/content/10.1101/2024.12.19.629313v1

In case you missed it. My colleague sneaked out a @biorxivpreprint.bsky.social just before Christmas with an insane amount of HQMAGs from soil using a looooot of @nanoporetech.com data. Data should be public already. Have fun 🎉 www.biorxiv.org/content/10.1...

Every PI should gift their phd students a @nanoporetech.com P2S starter pack before it goes from ~10k USD to 28k$ (January 29). What amazing research project would you do with 8 promethion flowcells? 🎁🧬🚀

Just unboxed a new @nanoporetech.com P2S. Somehow the ONT logo has moved since the first one we got. 🟩🟩🟩🟩🟩🟩🟩