MicroTrace: A Lightweight R Tool for SNP-Based Pathogen Clustering in Outbreak Detection
Kaitao Lai
TL;DR
MicroTrace is a lightweight R tool that facilitates SNP-based hierarchical clustering for pathogen outbreak detection, enabling epidemiologists to identify transmission clusters efficiently from whole-genome sequencing data.
Contribution
It introduces an open-source R package that simplifies SNP-based clustering workflows for outbreak detection with minimal setup.
Findings
Provides reproducible outbreak detection workflows
Outputs dendrograms and cluster tables with metadata integration
Supports efficient analysis of pathogen WGS data
Abstract
MicroTrace is an open-source R tool that performs SNP-based hierarchical clustering to detect potential transmission clusters from pathogen whole-genome sequencing (WGS) data. Designed for epidemiologists, microbiologists, and genomic surveillance teams, it processes SNP distance matrices and outputs dendrograms and cluster tables with optional metadata integration. MicroTrace enables reproducible outbreak detection workflows with minimal setup.
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