Vijini Mallawaarachchi

🔍 About the Phagefall game
In Phagefall, you control a bacteriophage inside a petri dish. The objective is to infect and lyse bacteria before they overrun the environment. (2/n)

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/...

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.

⭐ The code is fully open-source here: github.com/metagentools...
(stars help others discover it). All feedback welcome! (4/n)

🐍 Built using Pyodide + igraph + matplotlib — so Python + plotting logic all inside browser.

💡 Great for researchers working on metagenomic binning with assembly graphs — gives a quick, visual way to inspect improvements. (3/n)

🔗 Try it live: metagentools.github.io/graphbin-vis...

🧬 Upload your binning results + assembly graph files and instantly see before/after plots — your data never leaves your computer. (2/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.

🚀 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 - 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

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...

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–...

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...

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!!! 🎉🎉🎉

agtools: a software framework to manipulate assembly graphs Summary 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 g...

You can check out the agtools preprint on bioRxiv for more details and analysis.
doi.org/10.1101/2025...

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

Thanks for the capture! 😀

🧬 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

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...

Thanks mate

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

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

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...

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

🌟 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

A big shoutout to my amazing co-authors @rrwick.bsky.social @gbouras13.bsky.social @susiegriggo.bsky.social @npbhavya.bsky.social and @linsalrob.bsky.social. (6/n)

GitHub - Vini2/agtools: A Software Framework to Manipulate Assembly Graphs A Software Framework to Manipulate Assembly Graphs - Vini2/agtools

agtools is open-source and ready to drop into your own pipelines — feedback, issues, and contributions very welcome.

Github: github.com/Vini2/agtools

All you need to know about agtools can be found in the online documentation with lots of examples at agtools.readthedocs.io (5/n)

agtools exposes a Python package interface to load, query and analyse assembly graphs from popular genome and metagenome assemblers. Now you don't have to write custom code to load assembly graphs into your analyses. (4/n)

agtools provides a command-line interface for tasks such as assembly graph format conversion, segment filtering, segment renaming, graph concatenation and component extraction. (3/n)

Assembly graphs power assemblers and have become increasingly important in downstream applications like metagenomic binning, plasmid & viral resolution, and haplotype phasing — but tools providing programmatic access to assembly graphs are scarce. agtools gives you a CLI + Python API for this. (2/n)

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...

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

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

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...