Vijini Mallawaarachchi

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...

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...

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 https://www.biorxiv.org/content/10.1101/2025.08.05.668817v1

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

🚀 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

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

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...

🚨 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...

A man smiles at a lectern, talking towards a room. Behind him, a PowerPoint screen is shown with a blue background and the words 'AlphaFold Education Summit. 14 – 16 January 2025. Hinxton, United Kingdom. The EMBL's European Bioinformatics Institute and Google DeepMind logos are also shown on screen.

Earlier this year, with Google DeepMind, we held the AlphaFold Education Summit to increase and strengthen global capacity through train-the-trainer sessions & the co-development of further #AlphaFold training.

Now, we can share the free course materials with you: www.ebi.ac.uk/training/mat...
🧪🖥️🧬

Check out our latest publication, GraphBin-Tk, an assembly graph-based metagenomic binning toolkit.