bioRxivagtools: a software framework to manipulate assembly graphs https://www.biorxiv.org/content/10.1101/2025.09.14.676178v1?med=mas
| GITHUB | github.com/Vini2 |
Vijini Mallawaarachchi
- 39 Followers
- 35 Following
- 26 Posts
Research Associate at Flinders University | Bioinformatician exploring bacteria, phages and fungi in metagenomes 🧬🦠 | Blogging at http://vijini.medium.com
🧬 Check out agtools, an open-source Python framework for analysing & manipulating assembly graphs.
🔗 GitHub: https://github.com/Vini2/agtools
📜 Preprint: https://www.biorxiv.org/content/10.1101/2025.09.14.676178v1
🙏 Thanks to my amazing co-authors @rrwick @GB13Faithless @griggo_grig @npbhavya @linsalrob
#Bioinformatics #genomics #assembly #assemblygraphs #software
🚀 I just released agtools – a Python API + CLI for working with assembly graphs!
⚙️ Convert, filter, clean, visualise & more.
📦 Install with pip or conda
💻 Code: https://github.com/Vini2/agtools
📖 Docs: https://agtools.readthedocs.io/
⭐ Feedback, contributions, and stars are welcome!
#bioinformatics #python #genomics #assemblygraphs #opensource
📢 Excited to announce that Phables now supports long-read assemblies!
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⭐️ Check out the new release: https://github.com/Vini2/phables/releases/tag/v1.3.0
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🧬 Feel free to test out Phables on your long-read assemblies of metagenomes, viromes or even isolates. 🦠🧫
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#Phages #Bacteriophages #Phables #Metagenomics #Bioinformatics #Software
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⭐️ Check out the new release: https://github.com/Vini2/phables/releases/tag/v1.3.0
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🧬 Feel free to test out Phables on your long-read assemblies of metagenomes, viromes or even isolates. 🦠🧫
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#Phages #Bacteriophages #Phables #Metagenomics #Bioinformatics #Software
Excited to share that we were awarded a 2024 National Computational Merit Allocation Scheme (NCMAS) supercomputing grant. 🖥️🥳🤩
@linsalrob @BeardyMcJohnFace @npbhavya @griggo_grig
Glad to see GraphBin contributing to discover new core genera in fermented red pepper sauce metagenomes.
#bioinformatics #metagenomics #binning #assemblygraphs
https://www.sciencedirect.com/science/article/pii/S221242922301074X
It was my great pleasure to talk about Phables at ABACBS 2023. Thanks for all the awesome feedback and chats! Also a big thank you to @abacbs for the opportunity and everyone from the FAME lab.
#abacbs2023 #bioinformatics
#abacbs2023 #bioinformatics
I'm very excited to share that our bacteriophage recovery tool, Phables has been accepted for publication in the OUP Bioinformatics journal.
Publication: https://doi.org/10.1093/bioinformatics/btad586
GitHub: https://github.com/Vini2/phables
A big thank you to everyone at FAME for supporting this work.
@BeardyMcJohnFace @npbhavya @griggo_grig @GB13Faithless @AbbeyHutton @Sassel1985 @linsalrob
#bioinformatics #metagenomics #bacteriophages #assembly #assemblygraph #graphtheory #flownetworks
@griggo_grig from presenting Phynteny at APG Awards Fest. 🧬🦠🔬🌟 You can predict the functions of unknown phage genes using an LSTM model trained with phage synteny.
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Check out Phynteny at https://github.com/susiegriggo/Phynteny
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#phages #bacteriophages #synteny #APGAwardsFest2023
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Check out Phynteny at https://github.com/susiegriggo/Phynteny
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#phages #bacteriophages #synteny #APGAwardsFest2023
GitHub - susiegriggo/Phynteny: Predict the function of phage hypothetical proteins using an LSTM model trained with Phage Synteny
Predict the function of phage hypothetical proteins using an LSTM model trained with Phage Synteny - GitHub - susiegriggo/Phynteny: Predict the function of phage hypothetical proteins using an LSTM...
Excited to announce that the first stable release of Phables is now up on bioconda and PyPI. 🤩🧬 If you study phages in metagenomes give it a try. 😄
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Bioconda: https://anaconda.org/bioconda/phables
PyPI: https://pypi.org/project/phables/
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#Bioinformatics #metagenomics #phage #phage #bacteriophage
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Bioconda: https://anaconda.org/bioconda/phables
PyPI: https://pypi.org/project/phables/
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#Bioinformatics #metagenomics #phage #phage #bacteriophage