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.

Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols www.nature.com/articles/s41...

The new version of the protocol can be found at: www.protocols.io/view/pan-mic... A big thank you for all the hard work from all sites involved! (3/3)

Three decades of biodiversity data, published one decade after we started the project! Our new paper in @NatureComms shows how airborne eDNA from archived aerosol filters can track ecosystem changes across the tree of life—2700+ genera, weekly resolution, 34 years. www.nature.com/articles/s41...

Interested in virome sequencing on @nanoporetech.com instruments? Check out our latest paper where we publish Twist-ONT, a modified protocol for the Twist Comprehensive Viral Research Panel (by @twistbioscience.com) so that it can be used with ONT. www.sciencedirect.com/science/arti... 🧵1/7 🧪

As part of our Technical Blogs, Postdoc Researcher Ned Peel shares a step-by-step guide for using MARTi software, from initial setup through to interactive exploration. MARTi is an #opensource software tool for real-time analysis and visulisation of #nanopore #metagenomics. 💻🧬

Think you need large volumes for microbial experiments? Our recent publication introduces HiMEx, a simple, scalable method for microbial ecology. academic.oup.com/ismecommun/a... 🦠 it provides an easy, efficient approach to capturing viral diversity, opening new opportunities for virome analysis.

Most plasmids described in E. coli are small compared to the megaplasmids we identified here! Check out the preprint if you want to learn about these mysterious large elements and their potential functions 🧬. I’m very grateful to have had the opportunity to work on this in @banfieldlab.bsky.social

github.com/bede/deacon For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️

The GTDB website now has an ANI calculator based on skani that supports uploading of user genomes. Try it at gtdb.ecogenomic.org/tools/skani. Find more information about @jimshaw.bsky.social fantastic tool at www.nature.com/articles/s41....

The recordings of the 6-hour webinar on Bacterial Strain Taxonomy for Genomic Surveillance are now available through the @ecdc.europa.eu ECDC Learning portal: learning.ecdc.europa.eu/course/view.... - cgMLST, SNPs, K-mer based strain nomenclatures applications and more!

AlienDiscover: 🆕 v0.3 available to infer alien oligos (adapter, index, barcode, heteropolymer, ...) from #FASTQ files ✅ new confidence score for each inferred #long-read alien oligos ✅ ability to filter out #long-read alien oligos with low score ✅ still fast gitlab.pasteur.fr/GIPhy/AlienDiscover

If you want an example of gold standard genomics across every aspect of a paper, read this. It levelled me up. Covers #Acinetobacter baumannii. Recontextualises the global pop + reveals genuine insights. Includes development of software which types genomes too. www.nature.com/articles/s41...

📣 Open position: We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️ The scientific lead will be responsible for guiding the development of this important resource and for curating the SILVA taxonomy🌳and more! 👉 www.dsmz.de/dsmz/career/... Read and share ‼️ #sciencejobs 🦠🧪

Alignoth: portable and interactive visualization of read alignments academic.oup.com/bioinformati... 🧬🖥️🧪 Code (Rust, MIT): github.com/alignoth/ali... Demo: alignoth.github.io/preview.html

💾 any2fasta 0.8.1 is released! The FASTA format is now 40 years old (Pearson & Lipman) and any2fasta makes it easy for your scripts and pipelines that accept FASTA to also accept other formats, even if compressed! eg. .gbk.gz #bioinformatiocs #microbiology #genomcs github.com/tseemann/any...

Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm

💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...

ColabPCR: A validated Google Colaboratory Notebook for Reproducible and Precise Primer Design. www.biorxiv.org/content/10.6... 🧬🖥️🧪 github.com/maurijlozano... colab.research.google.com/github/mauri...

Beautiful blue #mosquito for your Bsky 🟦 🦟 #Sabethes (Culicidae) Soltis Center, Costa Rica (August)

Nice paper on the role of carnivorous plants in mosquito pest control. Aquatic plants of the genus Utricularia are equipped with suction traps (bladders, utricles) that are effective in trapping the early larval instars of mosquitoes. Paper: academic.oup.com/jme/article/...

Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇

SPARKI: a tool for the statistical analysis of pathogen identification results academic.oup.com/bioinformati... 🧬🖥️🧪 #Rstats code: github.com/team113sange... #Nextflow workflow: github.com/team113sange...

Are authors fairly judged by assessing the #journals in which their work is published? @bihutchins.bsky.social &co reveal that most influential papers are published in lower tier journals, and more authors would be better recognized with #ArticleLevelMetrics #ALMs @plosbiology.org 🧪 plos.io/4oV58Ed

Bioinformatics workbook bioinformaticsworkbook.org/#gsc.tab=0

How do you long-read sequence metagenomes? I would argue it starts with the right sample storage & DNA extraction, to enable efficient @nanoporetech.com /@pacbio.bsky.social sequencing, which we investigated in our new paper: www.biorxiv.org/content/10.1... Massive thanks to Klara for driving this

Excited to share that our paper on the relationship between viral load and metagenomic outputs in wildlife samples is now published in Microbial Genomics @microbiologysociety! 🎉 Fantastic collaboration with a brilliant team. More info: 📖 tinyurl.com/ywb7tvjm

#OneHealthResearch 🚨 New scoping review on climate & arboviruses in Australia: 📊 30 studies analysed 🌏 Inland regions included 🌡️ Temperature–infection link varied by region 👉 Highlights need to enhance human & 🦟 vector surveillance #RossRiverVirus #BarmahForestvirus

Viruses are found in almost every ecosystem across the planet. Now, researchers have released VIRE – a comprehensive viral genome database covering diverse ecosystems to advance understanding of viral evolution and ecosystem functions. Learn more: www.embl.org/news/science...

Happy to announce VIRE, a planetary-scale database of >1.7M viral genomes reconstructed from 100k+ metagenomes across diverse environments! In collaboration with @fullam.bsky.social, @tsbschm.bsky.social, and @borklab.bsky.social. academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1225/8356007

We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes. Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8

Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social doi.org/10.1093/bioa... The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives. More information on globdb.org 1/5 🖥️🧬🦠

🧫 Just out in Bioinformatics Advances: “GlobDB: A comprehensive species-dereplicated microbial genome resource.”  Explore the full study: https://doi.org/10.1093/bioadv/vbaf280

Folks been asking for a searchable catalogue for microbinfie podcast. With a 147 episodes, and 78+ guests its getting hard to find episodes of your interest. anyway, i wrote a catalogue https://www.happykhan.com/microbinfie see all our lovely guests at https://www.happykhan.com/microbinfie/guests

From #OUP 's #DATABASE journal | Automated annotation and validation of human respiratory #virus sequences using VADR | #Bioinformatics #Genomics #OpenScience #OpenSource 🧬 🖥️ 🧪 🔓 ⬇️ academic.oup.com/database/art...

In this Nature Medicine paper, we draw from our experiences in evaluating and implementing #genomics in Australia, Canada, England, Hong Kong and the US www.nature.com/articles/s41...

From the @ucscgenomics.bsky.social team in @natureportfolio.nature.com #scientificdata | Making genomic data FAIR through effective Data Portals | #FAIR #OpenScience #Bioinformatics #Genomics 🧬 🖥️ 🧪 🔓 CC/ @ebi.embl.org @mdperry.bsky.social ⬇️ www.nature.com/articles/s41...

Come see my poster at IMMEM Poster 151. 🔬 QualiBact – provides robust, data-driven QC thresholds for 304 bacterial species, built from >2.4M assemblies (AllTheBacteria + RefSeq). ⚙️ SpecCheck – an open-source command-line tool that applies these standards […] [Original post on mstdn.science]

🎉 Excited to announce that the 25th Annual Scientific Meeting of the Australian Society for Antimicrobials – Antimicrobials 2026 – will be held from 26–28 February 2026 at the Adelaide Convention Centre 📅 Save the date and stay tuned for program highlights!

Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b...

🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...

📢Health alert: #JapaneseEncephalitis virus detected in mosquitos in rural Victoria (Horsham), the first detection in the 2025/26 season Protect yourself: ✔️ Repellent ✔️ Cover up ✔️ Avoid dawn/dusk bites Free vaccine for high-risk groups More info: bit.ly/4omYE0l

Registration is now open! 🎉 Be part of the 2026 One Health Microbiome Center Symposium at Penn State (May 13–14). Explore microbiomes across health & ecosystems and connect with top researchers. Sign up here: www.eventbrite.com/e/2026-one-h...

Last chance! Early abstracts & travel awards for #ASMicrobe close TOMORROW (Dec 2, 2 p.m. ET). Early submissions receive early review—helpful for planning travel & approvals. Submit today! ➜ asm.social/2Ij

Final presentation by Calum J. Walsh @calumwalsh.bsky.social Rational Engineering of Live Bacterial Therapeutics from a Human Microbiome Biobank

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change. Ie: it's not us (Samtools team)! Be warned

GcMeta - a new global resource of metagenome-assembled genomes and their encoded functions with an easy to use, interactive and searchable website academic.oup.com/nar/advance-...

In the meantime, we've been collecting a list of these at tinyurl.com/mag-collecti.... Feel free to add more you find. See also GlobDB from @daanspeth.bsky.social which incorporates some of these into a new MAG collection arxiv.org/abs/2506.11896

Still using 16S/ITS profiling? You might want to reconsider👀 Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable! microbiomejournal.biomedcentral.com/articles/10....

Great to see this finally published! Metalog: curated and harmonised contextual data for global metagenomics samples now out in @narjournal.bsky.social academic.oup.com/nar/advance-...