FastMLST

FastMLST performs multilocus sequence typing (MLST) on draft genome assemblies to assign sequence type (ST) identifiers from allelic sequences for intra-species epidemiological and evolutionary analyses.

Key Features:

• Multi-Core Processing: Uses a divide-and-conquer approach with BLASTn to distribute MLST analyses across multiple CPU cores and perform typing on thousands of genome assemblies simultaneously, achieving at least a fourfold reduction in processing time compared to mlst, CGE/MLST, MLSTar, and PubMLST.
• PubMLST searches with BLASTn: Executes PubMLST database searches using BLASTn for allele matching and ST assignment.
• High Consistency: Produces ST assignments with greater than 99.95% consistency relative to traditional methods.
• Efficiency for Large Datasets: Optimized for processing large genomic datasets to support high-throughput MLST analyses.

Scientific Applications:

• Epidemiological surveillance: Assigns STs to support tracking of pathogen spread and outbreak investigations at the intra-species level.
• Evolutionary studies: Enables comparison of allelic profiles to infer genetic relationships and population structure within species.
• Public health monitoring: Facilitates large-scale genomic typing for surveillance programs and monitoring of clinically relevant strains.
• Microbial ecology: Supports characterization of intra-species diversity in environmental and ecological studies.

Methodology:

Conducts PubMLST searches using BLASTn and applies a divide-and-conquer strategy to distribute BLASTn-based MLST tasks across multiple CPU cores.