🚀 MetaCoAG v1.3.0 is out! This release adds faster FASTA processing, NumPy feature storage, better multiprocessing, cleaner graph traversal, and resumable runs. Benchmarks show up to 28.7x faster runtime and up to 56% lower peak memory. (1/n) #bioinformatics #metagenomics #assemblygraph

🎤 Very excited to be speaking at #GenomeInformatics26, UK from 2–4 December 2026. 🧬 📢 If you’re working in genome informatics or related areas, submit an abstract by 5 October 2026. Early bird registrations close on 7 September. 😃 #Bioinformatics #ComputationalBiology #Genomics #GenomeInformatics

Wellcome Connecting Science Learning and Training@eventswcs.bsky.social · 2mo ago

Register for our 26th #GenomeInformatics26 conference by 7 September for early bird savings! 🗓️ 2-4 December 2026 Bursary support available Explore the latest large-scale methods and AI-driven approaches that are advancing our understanding of genome structure and biology 🧬 📎 bit.ly/4bexmoH

If you do any work with DNA sequencing at some point, you need to assemble the reads. Usually, we just use the contigs, but that ignores important evidence from your data, so @vijinim.bsky.social wrote agtools to explore the assembly graph and learn more! academic.oup.com/bioinformati...

agtools: a software framework to manipulate assembly graphs

AbstractMotivation. Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap info

academic.oup.com

New preprint! 🚨 Phage proteins don't act alone. Phages rely on homooligomerisation to assemble identical protein subunits into functional forms. But figuring out those exact configurations experimentally is tough. Learn about our approach in our new preprint! 👇 (1/n) www.biorxiv.org/content/10.6...

🎉 Excited to share that our paper, “agtools: A Software Framework to Manipulate Assembly Graphs”, has been accepted in Bioinformatics Advances. (1/n) 🔗 GitHub: github.com/Vini2/agtools 📄 Paper: academic.oup.com/bioinformati... #bioinformatics #genomics #openscience

agtools: A Software Framework to Manipulate Assembly Graphs

AbstractMotivation. Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap info

academic.oup.com

🚀 Humbled to hit 1,000 citations on Google Scholar. Thank you to all the people who contributed, read, cited, challenged, and built on this work. #research #milestones #science scholar.google.com/citations?us...

Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...

Protein structure-informed bacteriophage genome annotation with Phold

Abstract. Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents.

academic.oup.com

George Bouras@gbouras13.bsky.social · 12mo ago

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

🚀 Just launched: GraphBin Visualise (WASM) a browser-based visualisation tool for comparing initial metagenomic binning results vs refined results from GraphBin - all running in your browser, no backend required. (1/n) #bioinformatics #metagenomics #binning #webapp #pyiodide #webassembly

GitHub - metagentools/graphbin-visualise-wasm-app: GraphBin Visualise WebAssembly App

GraphBin Visualise WebAssembly App. Contribute to metagentools/graphbin-visualise-wasm-app development by creating an account on GitHub.

github.com

This package to decompose weighted graphs into weighted paths by @alextomescu.bsky.social is going to be very useful. Can't wait to try it out in my viral metagenomic tools. 🤩🧬🖥️ #bioinformatics #graphs #graph-algorithms #flow-decomposition #integer-linear-programming github.com/algbio/flowp...

GitHub - algbio/flowpaths: A Python package to quickly decompose weighted graphs (acyclic or not) into weighted paths or walks, under various models.

A Python package to quickly decompose weighted graphs (acyclic or not) into weighted paths or walks, under various models. - algbio/flowpaths

github.com

Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years #phagesky www.nature.com/articles/s41...

Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature

Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...

nature.com

Thanks to the amazing Adelaide Bioinformatics community for making #ABACBS2025 an amazing event. We couldn’t have done it without you. A few more days of workshops to go before the festival finishes for another year 😀

Congratulations Hiruna Samarakoon (yet to be on bluesky) for winning the #abacbs2025 “Torsten Seemann” Outstanding Bioinformatics Software Developer Award!!! 🎉🎉🎉

It was great to present TRECA at ABACBS 2025 as a lightening talk. Come find my poster #21. #ABACBS2025 @abacbs.bsky.social

iplotx by Fabio Zanini supports visualising any network or tree analysis library. Can’t wait to visualise assembly graphs with iplotx! 🤩💻 #ABACBS2025 @abacbs.bsky.social

@rrwick.bsky.social solving all of our problems in long-read bacterial genome assembly with Autocycler. 😃🧬🦠 #ABACBS2025

🧬 Come check out my poster on agtools, an open-source Python framework for analysing and manipulating assembly graphs at #ABACBS2025 Poster #106 • 💻 Github: github.com/Vini2/agtools 📄 Preprint: biorxiv.org/content/10.110…

A gymnastic start to day 2 with a keynote from Ami Bhatt #ABACBS2025

Thanks mate Off the press just couple of hours before the talk www.nature.com/articles/s41...

Targeted sequencing and iterative assembly of near-complete genomes - Nature Communications

Long-read sequencing enables high-quality genome assemblies, but challenges remain. Here, the authors introduce Cornetto, a method that improves assembly quality, enables genome sequencing from saliva...

nature.com

Great opportunity! #ABACBS2025

What and incredible speaker! @zaminiqbal.bsky.social I really enjoyed learning all about bacterial plasmids and their evolution. PSA they are also recruiting in Bath UK - go talk to him for the deets #ABACBS2025

Excited to be at ABACBS 2025. Learning, connecting and growing. 😄🧬💻 #ABACBS2025

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n 📄 www.nature.com/articles/s41... 💿 mmseqs.com

GPU-accelerated homology search with MMseqs2 - Nature Methods

Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

nature.com

🌟 Exciting news! We’re launching three fully-funded postdoc positions for "New Horizons for Synthetic Phages” Join us in tackling antimicrobial resistance with cutting-edge synthetic biology + AI bioinformatics. Based at Flinders Uni in vibrant Adelaide. 👇 Read on for details! #Phage

Excited to share our latest preprint on agtools, an open-source Python framework for analysing and manipulating assembly graphs. (1/n) www.biorxiv.org/content/10.1... #Bioinformatics #genomics #assembly #assemblygraphs #software

agtools: a software framework to manipulate assembly graphs

Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap information, facilitating the assembler to construct longer genomic f...

biorxiv.org

I also put together an extra ColabFold formatted database of nearly 130M phage proteins that can be used to make better viral protein structure predictions github.com/gbouras13/co...

GitHub - gbouras13/colabfoldv: Augmented Local MSA Generation for Phage and Viral Proteins using the ColabFold Framework

Augmented Local MSA Generation for Phage and Viral Proteins using the ColabFold Framework - gbouras13/colabfoldv

github.com

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

Protein Structure Informed Bacteriophage Genome Annotation with Phold

Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...

biorxiv.org

Protein Structure Informed Bacteriophage Genome Annotation with Phold https://www.biorxiv.org/content/10.1101/2025.08.05.668817v1

🚀 I just released agtools – a Python API + CLI for working with assembly graphs! ⚙️ Convert, filter, clean, visualise & more. 📦 Install with pip or conda 📖 Docs & code: github.com/Vini2/agtools ⭐ Feedback, contributions, and stars are welcome! #bioinformatics #python #genomics #opensource

GitHub - Vini2/agtools: Tools for manipulating assembly graphs

Tools for manipulating assembly graphs. Contribute to Vini2/agtools development by creating an account on GitHub.

github.com

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

🚨 New preprint 🚨 My phage annotation tool, Phynteny, finally has a preprint and a brand new version powered by a cool AI transformer architecture and protein language models! #phagesky www.biorxiv.org/content/10.1...

Synteny-aware functional annotation of bacteriophage genomes with Phynteny

Accurate genome annotation is fundamental to decoding viral diversity and understanding bacteriophage biology; yet, the majority of bacteriophage genes remain functionally uncharacterised. Bacteriopha...

biorxiv.org