ViralMSA

ViralMSA performs reference-guided multiple sequence alignment of viral genomes to enable efficient, scalable alignment of large datasets for molecular epidemiology and transmission cluster identification.

Key Features:

• Scalability: Implements algorithms that scale linearly with the number of sequences, enabling processing of very large datasets.
• Read-mapper-derived algorithm: Leverages algorithmic techniques derived from read mappers to accelerate alignment computations.
• High-throughput performance: Capable of aligning tens of thousands of full viral genomes in seconds on suitable hardware.
• Reference-guided alignment: Produces alignments relative to a chosen reference genome to maintain positional consistency across sequences.
• Insertion handling: Alignments omit insertions relative to the reference genome.

Scientific Applications:

• Molecular epidemiology: Supports large-scale comparative analyses of viral genomes for studying evolutionary relationships and transmission dynamics.
• Transmission cluster identification: Enables rapid identification of clusters of related infections from large genomic datasets to inform outbreak investigations.
• Outbreak surveillance: Facilitates timely alignment of incoming viral genome sequences for tracking pathogen spread and informing public health responses.

Methodology:

Performs reference-guided alignment using techniques derived from read mappers, scales linearly with the number of sequences, and omits insertions relative to the reference.