Metagenomics colleagues! I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data. Please help and share!

Revio is a great product - it dramatically increased throughput over Sequel II (3x more data per cell, 12x more data per fully loaded run) and dropped the cost substantially. It's been the most successful instrument launch for the company, and now PacBio sequencing is at an all time high.

Beating our previous record by a wide margin I asked myself "Are @nanoporetech.com flowcells getting better?" 🚀🟩🧬 Let's find out! I created a form where you can register your yields so we can get a better overview. github.com/Kirk3gaard/O...

Did not expect to see disk space become an issue but after a disk clean up and restart I ended up with 243 and 244 gbp for these two @nanoporetech.com flowcells 🎉🚀🧬 💚🟩💚🟩💚🟩

After a day with almost 30 participants in the lab for our hands on @nanoporetech.com metagenomics course it is a blessing to see 🟩🟩🟩🟩🟩🟩🟩🟩🟩

@kirk3gaard.bsky.social , not recently active on Bluesky, on the 'tech bro' backing of Oxford @nanoporetech.com . We kind of already have a #techbro backing ONT, #LarryEllis who is one of the main investors and has put a ton of money into Oxford's EIT.

Please share this with anyone who may be interested in a post-doc in Germany: jobs.awi.de/Vacancies/20... This is quite an exciting opportunity to push the boundaries of what is known regarding the molecular basis of the formation and demise of photosymbiotic relationships in marine habitats.

Anyone else seeing @nanoporetech.com flowcells starting to "die" exactly around 72 hours? Could this be voltage control not being optimised for longer durations?

Preprint: Comparing BONCAT and MAR. Pro tips: don't buy the ClickIT kit, it's 25x overpriced as compared to buying individual chemicals by themselves (see my 2015 protocol chapter) and making reagents fresh gives superior results. And yes, only use picolyl dyes, my lab has been doing so since 2018.

How I like my @nanoporetech.com runs 🟩💚🟩🚀🧬

I'm recruiting a postdoc to figure out how aerobic methanotrophic bacteria oxidise methane in anoxic freshwater sediment environments: international.au.dk/about/profil... Come to Aarhus University in Denmark and work on this 2-year project funded by @villumfonden.bsky.social!

You load one @nanoporetech.com flowcell and it almost ruins your day 💩💩💩. You load six more and they look stunning 🟩💚🟩💚💚🟩

Still 10 days left to apply! 🦠🧪👩‍🎓🔬 Come work with my team in beautiful Vienna!

208Gb and can't tell you because it was for a customer @timdepooter.bsky.social

High yields are nice, but I think more important is highlighting the current robustness of the PromethION platform. In 2 weeks we processed 48 FC's resulting in 7.4Tb of data. That's over 150GB per FC on average. We definitely need to start thinking about mutliplexing. @nanoporetech.com

Professor (full) or Associate Professor (tenure track) in Microbial Genetics of Health (U. Turku Finland). Competitive starting package included! Please share. duunitori.fi/tyopaikat/ty...

193-200Gbp without any washing step (sewer biofilms & soil enrichments) ❇️🚀

Wow! I am very much against this. The deep value of GenBank is in it being a public domain database with 0 limitations on use. The norm that when we publish, we share the sequencing data supporting its claims *with 0 limitations on use* is so important for open science. I hope it doesn't change!

What is your highest yield on a @nanoporetech.com flowcell? And what was the sample type?

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