Kevin Bretscher

New blog post!

metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper:
rrwick.github.io/2025/09/23/a...

Both tools improved considerably! Time to update your conda environments 😄

Suprise delivery on Friday afternoon from @nanoporetech.com . Will be interesting to see if the Mk1D will increase flowcell output. #nanopore

We’re excited to welcome as keynote speakers for #PMS2025:

🪴 Lingfei Hu – Zhejiang University
💻 @jhcepas.bsky.social – CSIC & UPM

Join us in Malaga on 3-7 November!
Register now: 6thplantmicrobiomesymposium2025.com

#Plantscience #MicrobiomeResearch #Bioinformatics

#PMS2025 is going global! 🌍

So far, participants from 32 countries have registered for #PMS2025

This is your chance to connect, share ideas, and network with a international community of #plantmicrobiome scientists.

📅 Join now @ 6thplantmicrobiomesymposium2025.com

#MicrobiomeResearch

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!

Nanopore's getting accurate, but

1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?

with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social

1 / N

Figure 2 in Pantigoso et al. (2025): "Drought-induced shifts in root microbiome and metabolome."

New publication: Hub #metabolites at the root–microbiome interface: unlocking plant #drought resilience, by @vcarryon.bsky.social and others. #droughtresilience #climatechange #sustainableagriculture
doi.org/10.1016/j.tp...

This is figure 2, which shows M. ibericus queens lay males from two different species.

Living organisms are assumed to produce same-species offspring. A study in Nature reports a shift from this norm in Messor ibericus, an ant that lays individuals from two distinct species. go.nature.com/3V68MP0 🧪

We are happy to announce 2 more keynote speakers for #PMS2025!

We’re excited to welcome:

🔬 @gillesvanwezel.bsky.social – @unileiden.bsky.social
🦠 @iandealidbury.bsky.social – @sheffielduni.bsky.social

Join us at in Malaga on 3-7 November!
Register now: 6thplantmicrobiomesymposium2025.com

What happened 👀

Need bacterial DNA methylation data? Well, we’ve been re-basecalling all ONT data for the ATCC Genome Portal to get it. A huge effort, but as of today we have Mthyl data for ~1,500 bacterial strains. Attending #ASMicrobe? happy to chat IRL about it too. i.e. > genomes.atcc.org/genomes/67e8...

ICT medewerker in de serverruimte

Ben jij een ervaren Linux beheerder met een passie voor datamanagement en innovatie? Wil jij werken in een inspirerende wetenschappelijke omgeving waar je bijdraagt aan baanbrekend ecologisch onderzoek?

Solliciteer via onze website: nioo.knaw.nl/nl/vacatures...
#vacature #wageningen

🧫We are happy to announce 2 more keynote speakers for #PMS2025 bringing our total to 18 speakers!

We’re excited to welcome:

🔬 Harro Bouwmeester‬ – ‪UVA
🪴 Yang Bai – Peking University

Join us at #PMS2025 in Malaga on 3-7 November!

📅 Register now: 6thplantmicrobiomesymposium2025.com

Dorado is 1.0! 🎉

LC25 release adds v5.2 DNA/RNA models with a new suite of mod models that are higher accuracy, lower FP rates, and significantly faster.

- Introducing dorado variant 👀
- HAC error rate is down over 25%.
- New 2’Ome mod models
- Hopper & Blackwell SUP speed ups

#Nanoporeconf

A blueprint for contemporary studies of microbiomes - Microbiome This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opport...

🔎 Microbiomes under the microscope: A new scientific roadmap

📋 Published in #Microbiome

doi.org/10.1186/s401...

🌱 2 More Keynote Speakers for #PMS2025 🌱

🔬 ‪@asaflevylab.bsky.social‬ – @hebrewuniversity.bsky.social
🌱 Ling Ding – DTU ‪@dtu.dk‬

Join us at #PMS2025 in Malaga on 3-7 November!

📅 Register now: 6thplantmicrobiomesymposium2025.com

#MicrobiomeResearch #SoilHealth #PlantScience #Bioinformatics

🚨 Dear 🌱microbiome friends, only 1 day is left to secure a ticket for #PMS2025 at a discounted price! Take advantage of early bird fees by registering now!

6thplantmicrobiomesymposium2025.com
#microbiology #plantscience #microbiome #Bacteria

@microsos.bsky.social

*1 day

Great opportunity for PhDs and Students joining #PMS2025

🚨 Dear 🌱 microbiome friends, only 12 days are left to secure a ticket for #PMS2025 at a discounted price! Take advantage of early bird fees by registering now!
6thplantmicrobiomesymposium2025.com
#microbiology #plantscience #microbiome #Bacteria

@niooknaw.bsky.social

🌱 Two More Keynote Speakers for #PMS2025 🌱

🔬 @finkel-lab.bsky.social – @hebrewuniversity.bsky.social
🌱 Eiko Kuramae – NIOO

Join us at #PMS2025 in Malaga, November 2025.

📅 Register now: 6thplantmicrobiomesymposium2025.com

#PlantMicrobiome #MicrobiomeResearch #SoilHealth #PlantScience

🚨 Early Bird Deadline Extended!!!🚨

Due to high demand from early-career scientists, we’re extending the early bird registration and abstract submission deadline for #PMS2025 to May 15! 💡🌱

📅 Register here to reserve your spot at a discounted rate : 6thplantmicrobiomesymposium2025.com

Announcing 2 more Keynote Speakers for #PMS2025!

🍄 @vivianecordovez.bsky.social – @niooknaw.bsky.social

🌍 Juan Esteban Pérez-Jaramillo – University of Antioquia

📅 Abstract submission is open: 6thplantmicrobiomesymposium2025.com
#PlantMicrobiome #MicrobiomeResearch #PMS2025

🌱 This week we introduce two more Keynote Speakers of the 6th Plant Microbiome Symposium 2025 (3-7 Nov 2025)! 🌱
🔬 Angela Sessitch – Austrian Institute of Technology
🧪 Paolina Garbeva – NIOO-KNAW
📅 Register here: 6thplantmicrobiomesymposium2025.com
#PlantMicrobiome #MicrobiomeResearch #PMS2025

Roche Xpounds on New Sequencing Technology Bar bets can be a powerful force in human society.  One of the best known books on the planet, The Guinness Book of World Records, originate...

Roche Xpounds on New Sequencing Technology

My deep dive on this exciting new entrant

omicsomics.blogspot.com/2025/02/roch...

🧬🖥️

Abstract - 6th plant microbiome symposium 2025 The official language of the Symposium is English and the deadline for abstract submission is 28th april Download poster/oral abstract template here and an example abstract here. The format and guidel...

Call for abstracts

We are pleased to announce that abstract submissions for #PMS2025 has opened. This is a great opportunity to present your research and engage with leading experts in #plant #microbiomes.🦠🌿
Deadline: 28th April
Submit your abstract: 6thplantmicrobiomesymposium2025.com/abstract/

🌱 Our First Keynote Speakers for the Plant Microbiome Symposium 2025! 🌱
🌿 Prof. Julia Vorholt – ETH Zürich
🦠 Prof. Akos T. Kovács – Leiden University
Join us in Antequera on 3-7 Nov. Stay tuned for more announcements next week.

📅 Register now: 6thplantmicrobiomesymposium2025.com
#PMS2025 #microsos

I will look into predicted frameshifts. The main "issue" I have is that we sometimes see that a complete genome/contig can be assembled and closed with only 25X coverage. And I'm just wondering how much an assembly like that can be trusted.

Interesting read! How would you normally check the quality of a nanopore-only assembly (without reference) beyond tools such as CheckM/Busco or predicting the number of proteins with prokka?

A right that makes sense.