Benchmark update: metaMDBG and Myloasm
a blog for miscellaneous bioinformatics stuff
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 ๐
23.09.2025 01:53 โ ๐ 35 ๐ 26 ๐ฌ 4 ๐ 0
Suprise delivery on Friday afternoon from @nanoporetech.com . Will be interesting to see if the Mk1D will increase flowcell output. #nanopore
12.09.2025 16:47 โ ๐ 14 ๐ 1 ๐ฌ 0 ๐ 0
Weโre excited to welcome as keynote speakers for #PMS2025:
๐ชด Lingfei Hu โ Zhejiang University
๐ป @jhcepas.bsky.social โ CSIC & UPM
Join us in Malaga on 3-7 November!
Register now: 6thplantmicrobiomesymposium2025.com
#Plantscience #MicrobiomeResearch #Bioinformatics
12.09.2025 09:08 โ ๐ 11 ๐ 8 ๐ฌ 1 ๐ 1
#PMS2025 is going global! ๐
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.
๐
Join now @ 6thplantmicrobiomesymposium2025.com
#MicrobiomeResearch
09.09.2025 11:29 โ ๐ 11 ๐ 8 ๐ฌ 1 ๐ 0
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
07.09.2025 23:34 โ ๐ 113 ๐ 79 ๐ฌ 5 ๐ 5
Figure 2 in Pantigoso et al. (2025): "Drought-induced shifts in root microbiome and metabolome."
New publication: Hub #metabolites at the rootโmicrobiome interface: unlocking plant #drought resilience, by @vcarryon.bsky.social and others. #droughtresilience #climatechange #sustainableagriculture
doi.org/10.1016/j.tp...
05.09.2025 09:28 โ ๐ 12 ๐ 7 ๐ฌ 1 ๐ 1
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 ๐งช
07.09.2025 19:14 โ ๐ 61 ๐ 22 ๐ฌ 4 ๐ 3
We are happy to announce 2 more keynote speakers for #PMS2025!
Weโre excited to welcome:
๐ฌ @gillesvanwezel.bsky.social โ @unileiden.bsky.social
๐ฆ @iandealidbury.bsky.social โ @sheffielduni.bsky.social
Join us at in Malaga on 3-7 November!
Register now: 6thplantmicrobiomesymposium2025.com
02.09.2025 15:16 โ ๐ 9 ๐ 5 ๐ฌ 1 ๐ 0
What happened ๐
02.09.2025 08:43 โ ๐ 0 ๐ 0 ๐ฌ 1 ๐ 0
ATCCยฎ 9945aโข | Bacillus paralicheniformis | ATCC Genome Portal
Bacillus paralicheniformis is a strain of bacteria in the Bacillus genus. This genome was published to the ATCC Genome Portal on 2022-04-02
Need bacterial DNA methylation data? Well, weโve 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...
19.06.2025 20:39 โ ๐ 30 ๐ 9 ๐ฌ 2 ๐ 1
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
03.06.2025 11:32 โ ๐ 1 ๐ 3 ๐ฌ 0 ๐ 0
๐งซWe are happy to announce 2 more keynote speakers for #PMS2025 bringing our total to 18 speakers!
Weโre excited to welcome:
๐ฌ Harro Bouwmeesterโฌ โ โชUVA
๐ชด Yang Bai โ Peking University
Join us at #PMS2025 in Malaga on 3-7 November!
๐
Register now: 6thplantmicrobiomesymposium2025.com
23.05.2025 12:10 โ ๐ 10 ๐ 4 ๐ฌ 0 ๐ 0
Dorado is 1.0! ๐
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 ๐
- HAC error rate is down over 25%.
- New 2โOme mod models
- Hopper & Blackwell SUP speed ups
#Nanoporeconf
21.05.2025 17:14 โ ๐ 18 ๐ 8 ๐ฌ 0 ๐ 0
๐ฑ 2 More Keynote Speakers for #PMS2025 ๐ฑ
๐ฌ โช@asaflevylab.bsky.socialโฌ โ @hebrewuniversity.bsky.social
๐ฑ Ling Ding โ DTU โช@dtu.dkโฌ
Join us at #PMS2025 in Malaga on 3-7 November!
๐
Register now: 6thplantmicrobiomesymposium2025.com
#MicrobiomeResearch #SoilHealth #PlantScience #Bioinformatics
19.05.2025 15:53 โ ๐ 10 ๐ 7 ๐ฌ 1 ๐ 0
๐จ Dear ๐ฑmicrobiome 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
14.05.2025 15:57 โ ๐ 3 ๐ 2 ๐ฌ 1 ๐ 0
*1 day
14.05.2025 15:43 โ ๐ 1 ๐ 0 ๐ฌ 0 ๐ 0
Great opportunity for PhDs and Students joining #PMS2025
05.05.2025 13:24 โ ๐ 1 ๐ 0 ๐ฌ 0 ๐ 0
๐จ Dear ๐ฑ 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
02.05.2025 16:29 โ ๐ 15 ๐ 10 ๐ฌ 1 ๐ 0
@niooknaw.bsky.social
29.03.2025 16:42 โ ๐ 2 ๐ 0 ๐ฌ 0 ๐ 0
๐ฑ Two More Keynote Speakers for #PMS2025 ๐ฑ
๐ฌ @finkel-lab.bsky.social โ @hebrewuniversity.bsky.social
๐ฑ Eiko Kuramae โ NIOO
Join us at #PMS2025 in Malaga, November 2025.
๐
Register now: 6thplantmicrobiomesymposium2025.com
#PlantMicrobiome #MicrobiomeResearch #SoilHealth #PlantScience
28.03.2025 14:29 โ ๐ 16 ๐ 11 ๐ฌ 1 ๐ 1
๐จ Early Bird Deadline Extended!!!๐จ
Due to high demand from early-career scientists, weโre extending the early bird registration and abstract submission deadline for #PMS2025 to May 15! ๐ก๐ฑ
๐
Register here to reserve your spot at a discounted rate : 6thplantmicrobiomesymposium2025.com
18.03.2025 12:57 โ ๐ 5 ๐ 3 ๐ฌ 0 ๐ 0
Announcing 2 more Keynote Speakers for #PMS2025!
๐ @vivianecordovez.bsky.social โ @niooknaw.bsky.social
๐ Juan Esteban Pรฉrez-Jaramillo โ University of Antioquia
๐
Abstract submission is open: 6thplantmicrobiomesymposium2025.com
#PlantMicrobiome #MicrobiomeResearch #PMS2025
06.03.2025 13:28 โ ๐ 12 ๐ 4 ๐ฌ 0 ๐ 0
๐ฑ This week we introduce two more Keynote Speakers of the 6th Plant Microbiome Symposium 2025 (3-7 Nov 2025)! ๐ฑ
๐ฌ Angela Sessitch โ Austrian Institute of Technology
๐งช Paolina Garbeva โ NIOO-KNAW
๐
Register here: 6thplantmicrobiomesymposium2025.com
#PlantMicrobiome #MicrobiomeResearch #PMS2025
21.02.2025 14:40 โ ๐ 12 ๐ 6 ๐ฌ 0 ๐ 0
Abstract - 6th plant microbiome symposium 2025
The official language of the Symposium is English and theย deadline for abstract submission is 28th april Download poster/oral abstract template hereย 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.๐ฆ ๐ฟ
Deadline: 28th April
Submit your abstract: 6thplantmicrobiomesymposium2025.com/abstract/
14.02.2025 11:42 โ ๐ 10 ๐ 8 ๐ฌ 0 ๐ 0
๐ฑ Our First Keynote Speakers for the Plant Microbiome Symposium 2025! ๐ฑ
๐ฟ Prof. Julia Vorholt โ ETH Zรผrich
๐ฆ Prof. Akos T. Kovรกcs โ Leiden University
Join us in Antequera on 3-7 Nov. Stay tuned for more announcements next week.
๐
Register now: 6thplantmicrobiomesymposium2025.com
#PMS2025 #microsos
14.02.2025 11:33 โ ๐ 13 ๐ 6 ๐ฌ 0 ๐ 0
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.
09.02.2025 08:24 โ ๐ 1 ๐ 0 ๐ฌ 1 ๐ 0
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?
07.02.2025 06:24 โ ๐ 1 ๐ 0 ๐ฌ 1 ๐ 0
A right that makes sense.
09.01.2025 10:59 โ ๐ 1 ๐ 0 ๐ฌ 0 ๐ 0
Biotechnologist & Plant pathologist(MSc)
(Research assistant officer - Tanzania Agricultural research Institute- Tari)
#Biotechnology, molecular biology & microbiology
#Crop science #plant pathology
๐ฆ Currently working on Characterisation of Alternaria
New horizons. All omics. AgBio field NGS specialist. ๐ฑ ๐๐พ๐๐ป๐vegetables, field crops, berries and ornamentals. #DNA #RNA #protein
Microbiome, evolution, comparative genomics, biodiversity and a little bit of ecology: cgmlab.org
Group Leader at CBGP-CSIC/UPM in Madrid, former scientist at EMBL Heidelberg, CRG Barcelona and CIPF Valencia.
The Diamond Lab | Innovative Genomics Institute @ UC Berkeley | Metagenomics | Microbiome Systems Ecology and Modeling | AI for Microbes | Environmental MGEs | Health and Climate Change
@innovativegenomics.bsky.socialโฌ | @ucberkeleyofficial.bsky.social
Computational biology lab focusing on microbiomes in the human gut and the environment
Homepage: https://www.bork.embl.de/
Mastodon: https://mstdn.science/@BorkLab
Interested in the spatially organized interaction of physical and biochemical root barriers and the root microbiome ๐ฑ๐ฆ ๐งฌ๐ฌ
Professor in Microbiology at the University of Helsinki. Guitar in Insomnium. Honorary Fellow at the University of York and Honorary Professor at Nanjing Agricultural University
https://www.helsinki.fi/en/researchgroups/microbial-ecology-and-evolution
WP leader in EU Horizon Project BarleyMicroBreed, https://agro.au.dk/forskning/internationale-platforme/barleymicrobreed/about-barleymicrobreed
PI at BOKU https://boku.ac.at/en/wabo/ife/staff/root-phenomics-and-mechanomics
interested in root imaging
PubPeer is a platform for post-publication peer review, offering an additional layer of evaluation beyond journal names. Empowering the scientific community to assess science and scientists transparently. pubpeer.com
Tenured Scientist at IHSM La Mayora.
Leader of the Sustainable Agro-food Materials group.
Circular bioeconomy, bioplastics, food packaging.
Computational microbiologist
I like to post about: microbial genomics, microbial ecology, evolution, micro+plant biotechnology, climate, symbiosis, virology, ag, sci publishing and policy
Postdoc at Dana-Farber and Harvard Med with Heng Li (@lh3lh3.bsky.social). Prev: UBC / UofT.
I like thinking about computational biological sequence analysis and its applications to metagenomics.
https://jim-shaw-bluenote.github.io
Genome Plasticity and Computational Genetics.
We develop cutting-edge technologies to explore genome evolution!
Lab Website: https://schneebergerlab.org/
phylogenetics, molecular evolution, some genomes, kids, dogs, and eclectic hobbies none of which I am much good at but I think for me that's the point
Professor of Microbiology @ University of Innsbruck, Austria
Honorary Associate Professor @ The University of Queensland, Australia
Environmental OMICS (E-OMICS) team lead
http://www.rinkelab.org
(former twitter/x account: @ChristianRinke )
From ๐ช๐ธ, PhD student at University of Glasgow๐ด๓ ง๓ ข๓ ณ๓ ฃ๓ ด๓ ฟ studying Streptomyces spp. interactions in soil๐ฑ๐ฆ . Bioinformatics & Biostatistics MSc University of Barcelona.
https://www.linkedin.com/in/diag-alexandra