🔬 AMR-BERT Pipeline
(In development – expected Q1 2026)
End-to-end AMR prediction system combining Nextflow, assembly, QC, CARD, and DNABERT2 classification.
Tech: Python, PyTorch, DNABERT2, ESM2, Nextflow, Docker
🧬 Automated AMR Gene Detection Pipeline
(Completed)
SPAdes + Prokka + Abricate + custom QC modules; deployed with Docker and automated reporting.
Tech: SPAdes, Prokka, Abricate, Docker, Python, Bash
🧪 Nextflow WGS Processing Workflow
(In progress)
Modular DSL2 pipeline for bacterial assembly, annotation, AMR identification, phylogenomics.
Tech: Nextflow, nf-core, Docker, Prokka, FastTree, SNP-sites
🧠ML-Based Pathogen Classification from Reads
(In progress)
Binary and multi-class models trained on k-merized reads to classify bacterial species.
Tech: PyTorch, scikit-learn, FastAPI