Vijini Mallawaarachchi
@vijinim.bsky.social
Research Fellow @ Flinders University | #Bioinformatics and #Metagenomics 🧬🦠 | Blog at http://vijini.medium.com
Reposted by Vijini Mallawaarachchi
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
📄 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...
www.nature.com
September 21, 2025 at 8:06 AM
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
📄 www.nature.com/articles/s41...
💿 mmseqs.com
Reposted by Vijini Mallawaarachchi
🌟 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
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
July 25, 2025 at 8:15 AM
🌟 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
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
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...
www.biorxiv.org
September 17, 2025 at 6:58 AM
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
www.biorxiv.org/content/10.1...
#Bioinformatics #genomics #assembly #assemblygraphs #software
Reposted by Vijini Mallawaarachchi
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
August 8, 2025 at 7:14 AM
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...
Reposted by Vijini Mallawaarachchi
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...
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...
www.biorxiv.org
August 8, 2025 at 7:11 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Vijini Mallawaarachchi
Protein Structure Informed Bacteriophage Genome Annotation with Phold https://www.biorxiv.org/content/10.1101/2025.08.05.668817v1
August 7, 2025 at 3:47 AM
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
⚙️ 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
August 7, 2025 at 2:00 AM
🚀 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
⚙️ 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
Reposted by Vijini Mallawaarachchi
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
myloasm-docs.github.io
myloasm - metagenomic assembly with (noisy) long reads
myloasm-docs.github.io
May 28, 2025 at 5:54 PM
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
myloasm-docs.github.io
Reposted by Vijini Mallawaarachchi
🚨 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...
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...
www.biorxiv.org
July 30, 2025 at 6:01 AM
🚨 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...
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...
Reposted by Vijini Mallawaarachchi
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...
🧪🖥️🧬
Now, we can share the free course materials with you: www.ebi.ac.uk/training/mat...
🧪🖥️🧬
May 29, 2025 at 2:11 PM
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...
🧪🖥️🧬
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.
Just published in JOSS: 'GraphBin-Tk: assembly graph-based metagenomic binning toolkit' https://doi.org/10.21105/joss.07713
May 29, 2025 at 12:31 AM
Check out our latest publication, GraphBin-Tk, an assembly graph-based metagenomic binning toolkit.