❓ Do you develop a #nextflow pipeline for #metagenomics, #metataxonomics, #metatranscriptomics, #metaproteomics, etc? 🧑‍💻 I'm looking for #bioinformatics developers to give demos of their #opensource pipelines to the scientific community in a ‘Meta-*omics Nextflow pipeline community exhibition […]

Genetic variation is the key to species resilience, enabling populations to adapt to changing environmental conditions. Our research group will take a deep dive into the variation present in the genes encoding for central roles of the immune system. www.slu.se/en/news/2025...

New blog post! Introducing nf-core Advisories https://nf-co.re/blog/2025/advisories/

InterProScan 6 (beta) is here 🎉 A Nextflow-powered, containerised overhaul for scalable, reproducible protein annotation—decoupled software/data, automated data handling, and smoother runs across HPC and cloud. Feedback welcome! github.com/ebi-pf-team/... 💻🧪🧬

From @plos.org #Computational #Biology | Fundamentals of FAIR biomedical data analyses in the cloud using custom pipelines | #Bioinformatics #FAIR #Cloud #Education #OpenScience #Nextflow #WDL #CWL 🧬 🖥️ 🧪 🔓 ⬇️ journals.plos.org/ploscompbiol...

I’m really happy to present #SCALPEL, a new #Nextflow tool to quantify transcript isoforms at the single-cell level using conventional 3’ scRNA-seq data #scRNA-seq #single-cell #tools #isoforms www.nature.com/articles/s41...

From @drvgmartinacosta.bsky.social & colleagues in @plos.org #Computational #Biology | Ten simple rules for faculty members building just and equitable environments in academic science | #Education #PLOSCBTSR 🧬 🖥️ 🧪 🔓 ⬇️ journals.plos.org/ploscompbiol...

We have just released a new version of the Microbiome Informatics metagenomes assembler pipeline - github.com/EBI-Metageno.... Jenny Mattock benchmarked a new contigs cleaning process that Sonya Ochkalova implemented. Great team effort with > 100 comments in the PR. #nextflow @mgnifydb.bsky.social

Used EMBL-EBI data resources to find, analyse, or archive your data? 🧬 Now’s your turn: tell us how you’ve used them + why they matter. It takes 15 mins and helps keep these services open and free for all. 👉 tinyurl.com/bdf73zpp Closes 16 July #opendata #FAIRdata

My time as a Bioinformatics Staff scientist at CalTech is coming to a close and I am looking for the next thing. If you need someone with plenty of experience in sequencing analysis, and pipeline building (Nextflow), please connect. I'm hoping to go back to industry but open to anything interesting.

Colora: A Snakemake Workflow for Complete Chromosome-scale De Novo Genome Assembly www.biorxiv.org/content/10.1... 🧬🖥️ github.com/LiaOb21/colora

Some useful advice for sample collection to generate a reference genome. academic.oup.com/gigascience/...

You might know that @nf-co.re is crazy about @nextflow.io pipelines, but did you know that we're also mad about laptop stickers? 😆 We have a whole web page dedicated to them where you can see the whole collection so far: nf-co.re/stickers

New short blog: Setting up the @nextflow.io Language Server (LSP) with NeoVim livesys.se/posts/nextfl...

1/4: If you are at #IEEE #CCGrid 2025 in #Tromsø next week, catch Jonathan, Fabian, and Kathleen (@westkath.bsky.social) presenting joint work! 📰🧵👇 #CCGrid #distributed #sustainable #cloud #computing #research #Spark #Nextflow

We’ve just dropped some powerful new @nextflow.io features as part of the 25.04 release, all designed to enhance clarity, control, and collaboration in workflow development. 🎉 💡Learn more: hubs.la/Q03mQ2_10

In this (rebutted) grant proposal I wrote that I thought we could see circular RNAs with Vizitig, despite being hard to detect and with low expression. Guess what? Looks very much like a circular RNA to me 😎 (in TET2 gene, human co-assembled cancer RNA-seq samples).

Nice blog post by @charlottetolonen.bsky.social from a couple of weeks ago about how to use conda for #bioinformatics without running afoul of anaconda licensing: blog.fulcrumgenomics.com/p/anaconda-l... 🧬 🖥️

From a single researcher to global R&D teams, the needs stay the same: reliability, scalability, simplicity.

Junior faculty job alert in Germany - Marine Evolutionary Genomics @geomarkiel.bsky.social / University of Kiel www.geomar.de/en/karriere/... Marine study system of your choice (no microbes, sorry…), excellent infrastructure and ship access, moderate teaching requirements, closing date 6 June

Unique investigation of some errors in long read assemblers. In particular these remarkably chimeric contigs are 😱, if rare.... Improving long read assemblers is definitely the space to be in when it comes to the future of metagenomics, as short reads won't be part of it 😉

Continuing with @imartayan.bsky.social and Lucas Robidou presenting Hyper-k-mers a novel efficient streaming k-mers representation. A joint work with @npmalfoy.bsky.social and Yoshihiro shibuya

I learned so much in researching this article. Thanks, as always, to the many sources who were so generous with their time, not all of whom made it into the final article, inc. @titus.idyll.org @robp.bsky.social @gvwilson.bsky.social @noamross.net @yabellini.bsky.social and more.

@camillemrcht.bsky.social is back on stage to present Vizitig, an interactive visualization tool for sequencing datasets developped by @bdegardins.bsky.social

Vizitig: context-rich exploration of sequencing datasets www.biorxiv.org/content/10.1... 🧬🖥️🧪 gitlab.inria.fr/vizisoft/viz...

Discover Pixi Tasks! 🪄 Watch here: youtu.be/SW3yH9xZBTE

One day left to apply! Not seeing many American applications so far, which puzzles me a little bit. If you have a four-year degree including advanced courses in Ecology or Evolution, you are likely eligible. Happy to answer detailed questions over DM or email.

so they're mycoblogging

Annotation of 200 insect genomes. Work driven by @stepbystepsolution.bsky.social and Mario Stanke within @gevol.bsky.social : www.biorxiv.org/content/10.1...

Plenty of tortured phrases (arxiv.org/abs/2107.0...) in this #IEEE paper. ieeexplore.ieee.org/... My pubpeer report: pubpeer.com/publicat...

Really cool that the latest VSCode extension for Nextflow shows nf-test test coverage! 🚀

I put up another Nextflow Tips & Tricks on Seqera's Community Forum. How to skip specific/failed samples on the next resume. community.seqera.io/t/how-to-ski...

🎉Episode 50 of the @nextflow.io Podcast is here! Host @ewels.bsky.social sits down with @kbestak.bsky.social, a PhD student and active contributor to the @nf-co.re community, working at the cutting edge of #SpatialOmics and #microscopy. 🎧Catch it here: hubs.la/Q03fVPNx0

Had a great time chatting to @kbestak.bsky.social in today's podcast. It's really exciting to see how the #microscopy community (which is huge and varied) is warming to @nextflow.io - new pipelines sprouting up all over @nf-co.re! 🌱 🧫 🔬 If interesting, join the nf-core #microscopy Slack channel!

🚀 Discover Wave: on-demand container images for your pipelines 🔹Generate container images instantly, ready to use for your pipelines 🔹Natively integrated in your #Nextflow pipelines or via a user-friendly interface 🔹Permanently store containers, with infrastructure powered by AWS

THIS IS HUGE! Researchers at Stanford University have developed a dual-antibody treatment that remains effective against ALL SARS-CoV-2 variants by targeting a less-mutable part of the virus. This breakthrough could lead to longer-lasting therapies that OUTPACE viral evolution. 🧪🧵⬇️

We've been working really hard on the new Nextflow training materials and they've turned out great. Take advantage of them on your own or by doing a watch party with a group next week during our Nextflow training week. 🚀

🔬 Recently published: "SpaFlow: A Nextflow pipeline for QC and clustering of MxIF datasets" Read more online: https://doi.org/10.1093/bioadv/vbaf032 #SpatialBiology #Proteomics   (1/3)

Deadline for abstract submission is this Friday! Hope to see many of you (n=40) this June in Tübingen!

Applying the FAIR Principles to computational workflows https://www.nature.com/articles/s41597-025-04451-9 🧬🖥️🧪 Nextflow = batteries included 🔋

🚀 Introducing #Nextflow Training Week! A free, self-paced online training designed to help beginners get started with Nextflow. 📅 March 10-14, 2025 🎥 On-demand videos and real-time support 💬 Ask questions in our community forum Learn more and join us: hubs.la/Q038kTQm0

Policies are shaping how we access and process genetic data, how we work, and so much more. How? Camila Mazzoni and I co-wrote a @seqera.io blogpost to showcase the link between policies and bioinformatics! Go have a look and comment with any question or remarks 😊

If you are a BIA user or you are interested in using our service, please consider giving us feedback here: forms.gle/gcML5ZjMCDxp...

The DOGE firings have nothing to do with “efficiency” or “cutting waste.” They’re a direct push to weaken federal agencies perceived as liberal. This was evident from the start, and now the data confirms it: targeted agencies overwhelmingly those seen as more left-leaning. 🧵⬇️

Fantastic talk this afternoon by @joanameier.bsky.social! Joana discussed how hybridisation and chromosomal rearrangement facilitate adaptive radiation, using cichlids and Ithomiini butterflies as study systems 🐟🦋 We also learnt a bit about @projectpsyche.bsky.social! #evolution #speciation

Do you want to know more about git, conda, snakemake, nextflow, quarto, jupyter and containers? The Tools for reproducible research course is back! 7-11 April, 2025 in SciLifeLab Solna (Stockholm, Sweden). Apply here before March 7th: forms.gle/kmoEPbzWEnHb...

To US colleagues who have lost or are in imminent danger of losing their jobs: please DM whether we can accommodate your research.

Now seems a good time to mention that I haven't yet filled a postdoc position in phylogenetic methods. If you just lost your job, need something temporary, and know something about bioinformatics/statistics/evolution, talk to me.

Hey if anyone is considering backing up any datasets for some reason today, the Open Science Framework has free storage up to 5G/private repository, and up to 50G/public repository. (The OSF is run by a 501c3 (Center for Open Science), so if you do this you might also consider making a donation.)

Londonomics has made the move over to Bluesky 🦋 We now have 200+ members and we’re excited to bring you together at workshops, networking events, and the annual symposium! 💡 We’ll be kicking things off with a NextFlow workshop in March 👀