BacTag

BacTag performs rapid gene and allele typing from bacterial whole-genome sequencing (WGS) data to identify alleles for applications such as Multi Locus Sequence Typing (MLST) and subspecies classification.

Key Features:

• Efficient Database Preprocessing: Determines a representative reference sequence for each gene and stores variations of all known alleles relative to that reference.
• High Similarity Exploitation: Exploits high sequence similarity among alleles to avoid mapping reads against every individual allele reference, reducing computational time and resources while maintaining accuracy.
• Parallel Computing Integration: Implements parallel computing to accelerate processing of large-scale WGS datasets.
• Versatile Application Range: Validated on artificial WGS datasets from E. coli, S. pseudintermedius, P. gingivalis, M. bovis, Borrelia spp., and Streptomyces spp., and on real WGS data from E. coli and K. pneumoniae.

Scientific Applications:

• Bacterial Subspecies Classification: Identifies gene alleles to support subspecies-level classification and analyses of microbial diversity.
• Clinical Diagnostics: Rapidly detects specific alleles to inform diagnosis of bacterial infections.
• Epidemiological Studies: Provides allele-level genotypes to support outbreak tracking and population genetics investigations.

Methodology:

Preprocesses allele databases to select a representative reference sequence per gene and record allele variations relative to those references; maps sequencing reads against representative references instead of every allele; and applies parallel computing to speed analysis.