BactSNP

BactSNP identifies single-nucleotide polymorphisms (SNPs) among bacterial isolates from whole-genome sequencing (WGS) data by integrating assembly and mapping information to produce accurate SNP calls for downstream analyses such as phylogenetic inference.

Key Features:

• Assembly and mapping integration: Integrates both de novo assembly and read-mapping information to improve SNP detection accuracy.
• Single-step SNP calling: Performs SNP calling in a single step to achieve high sensitivity and accuracy for closely related bacterial isolates.
• Reference flexibility: Calls SNPs using draft genomes or in the absence of any input reference genome.
• Output formats: Produces a TSV file with detailed SNP information and an alignment FASTA file containing reconstructed pseudo-genomes of target isolates.
• False-positive reduction: Reduces false-positive SNP calls commonly observed with traditional SNP callers when analyzing closely related strains.

Scientific Applications:

• Outbreak investigation: Enables high-resolution comparison of closely related bacterial isolates for detection and tracking of outbreaks.
• Phylogenetic inference: Provides accurate SNPs for constructing phylogenetic trees and comparative analyses.
• Microbial genetics: Facilitates studies of bacterial diversity and population structure from WGS data.
• Epidemiology: Supports genotype-based surveillance and epidemiological investigations.
• Evolutionary biology: Assists analyses of microevolution within bacterial species.

Methodology:

Integrates assembly and read-mapping information to perform single-step SNP calling and outputs a TSV of SNPs and an alignment FASTA containing reconstructed pseudo-genomes.