usher

usher places new genome sequences onto existing phylogenies to enable rapid phylogenetic placement and real-time genomic contact tracing, particularly for SARS-CoV-2.

Key Features:

• Speed and Efficiency: Achieves orders-of-magnitude faster placement times than traditional methods, enabling real-time analyses.
• Memory Optimization: Uses memory-efficient data structures to support large-scale analyses without extensive computational resources.
• Versatility: Applicable beyond SARS-CoV-2 to a wide range of phylogenetic studies.
• Tree-based data structure: Encodes evolutionary history in an efficient tree-based data structure and maintains an updated reference phylogeny.
• Real-time placement: Enables rapid placement of new sequences into a growing phylogeny to support genomic contact tracing and ongoing surveillance.

Scientific Applications:

• Genomic Contact Tracing: Supports placement of viral genomes onto large phylogenies to infer transmission links and local transmission dynamics in near real-time.
• Data Visualization and Analysis: Accelerates phylogenetic placement to facilitate visualization and downstream analysis of viral evolution and spread.

Methodology:

Uses an efficient tree-based data structure to encode evolutionary history and places new samples onto an existing reference phylogeny, accelerating placement while maintaining the updated reference tree.