BlastFrost

BlastFrost queries compacted and colored de Bruijn graphs produced by Bifrost to rapidly identify genes and single nucleotide variants across collections of bacterial genome assemblies.

Key Features:

• Graph representation: Uses compacted and colored de Bruijn graphs from the Bifrost framework to represent bacterial genomes.
• Graph querying: Queries Bifrost-generated data structures to locate sequences of interest within genome assemblies.
• Local subgraph extraction: Extracts local subgraphs from the overall graph to support targeted sequence retrieval.
• Variant and gene detection: Facilitates precise detection of individual genes and single nucleotide sequence variants (SNVs).
• Scalability: Demonstrated ability to analyze large datasets, including identifying SPI-2 pathogenicity island genes across 926 Salmonella genomes in minutes and detecting SNPs associated with fluoroquinolone resistance in three genes among 190,209 genomes.

Scientific Applications:

• Gene presence/absence screening: Identification of genes within the SPI-2 pathogenicity island across Salmonella genome collections.
• Antimicrobial resistance SNP detection: Detection of SNPs associated with fluoroquinolone resistance in three specific genes across large genome datasets.
• Large-scale bacterial genome analysis: High-throughput interrogation of genetic variation and pathogenicity traits across extensive bacterial assembly collections.

Methodology:

Builds compacted and colored de Bruijn graphs using Bifrost, queries those graphs, and extracts local subgraphs to locate sequences and detect genes and SNVs.