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1. pathogen-discovery-pipeline pathogen-discovery-pipeline Public

   Panel driven metagenomic confirmatory mapping pipeline with host subtraction and competitive mapping for bacteria, viruses, fungi, and parasites

   Shell 1

2. ddns-minion-vp1-pipeline ddns-minion-vp1-pipeline Public

   Standalone ONT MinION VP1 analysis pipeline for DDNS stool-culture amplicon sequencing

   Python

3. pakistan-sars-cov-2-nextstrain-build pakistan-sars-cov-2-nextstrain-build Public

   Reproducible Pakistan SARS-CoV-2 Nextstrain build workflow

   Shell

4. polio-capsid-ngs-analysis polio-capsid-ngs-analysis Public

   Reproducible post-culture whole-capsid Illumina workflow for poliovirus. Reference-based consensus, antigenic site analysis across VP1-VP3, phylogeny, and optional de novo checks.

   Python

5. polio-wpv1-phylodynamics polio-wpv1-phylodynamics Public

   Reproducible WPV1 phylogeographic analysis template with synthetic example data

   R