OutbreakFinder

OutbreakFinder detects and visualizes bacterial strain clusters from next-generation sequencing-derived distance matrices, alignment outputs (Lyve-SET, Parsnp, ClustalOmega), or Newick trees to support outbreak detection and epidemiological investigations.

Key Features:

• Input Flexibility: Accepts distance matrices in CSV format, alignment files from Lyve-SET, Parsnp, and ClustalOmega, and tree files in Newick format.
• Multidimensional Scaling (MDS): Employs optimized multidimensional scaling (MDS) to reduce high-dimensional genetic distance or phylogenetic data into two-dimensional space while preserving relative distances.
• Two-dimensional Visualization: Produces two-dimensional plots that display relative relationships among isolates derived from phylogenetic or distance data.
• Affinity Propagation Clustering: Applies affinity propagation clustering to automatically identify and label clusters without requiring a predefined number of clusters.

Scientific Applications:

• Outbreak Detection: Rapid identification of epidemiologically related bacterial strain clusters from whole-genome sequencing data.
• Genomic Epidemiology: Visualization and clustering of NGS-derived genomic data to inform epidemiological investigations and public health responses.

Methodology:

Accepts CSV distance matrices, alignment files (Lyve-SET, Parsnp, ClustalOmega), or Newick trees; transforms phylogenetic/genetic distance data into two-dimensional plots via optimized MDS; and applies affinity propagation clustering to identify and label clusters.