Hi there 👋
I’m Vijini Mallawaarachchi—I’m a Research Fellow in Bioinformatics at the Flinders Accelerator for Microbiome Exploration, Flinders University. I enjoy developing algorithms, writing code, reading and blogging.
My current research work is focused on algorithms and computational models related to the construction of metagenome-assembled genomes (MAGs). Metagenomics involves the study of genetic material obtained from the genomes found in microbial communities. A microbial community can contain a large number of organisms. My work focuses on developing methods and tools to investigate the taxonomic structure of a given metagenomic sample.
- 🔭 I’m currently working on computational methods to resolve viral genomes
- 🌱 I’m currently exploring graph algorithms and graph machine-learning techniques
- 📫 How to reach me: viji.mallawaarachchi@gmail.com
- 🏠 Check out my personal website: https://vijinimallawaarachchi.com
- 📝 Check out my Medium Blog: https://vijini.medium.com/
Repo Highlights
✨🧬 GraphBin: Refined Binning of Metagenomic Contigs using Assembly Graphs
The first automated tool to make use of assembly graphs to refine binning results from existing metagenomic contig-binning tools.
☯️🧬 GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
Next generation of GraphBin that refines binning results from existing metagenomic contig-binning tools using assembly graphs. GraphBin2 also assigns contigs to multiple bins if they are shared between different species.
🚦🧬 MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs
The first stand-alone metagenomic contig-binning tool that makes use of assembly graphs apart from composition and coverage information for binning.
🫧🧬 Phables: from fragmented assemblies to high-quality bacteriophage genomes
Resolving high-quality bacteriophage genomes from fragmented assemblies of viral metagenomic data using graph algorithms and flow decomposition techniques.