ReferenceSeeker

ReferenceSeeker identifies appropriate reference genomes for microbial genomics analyses by rapid kmer profile-based lookup and computation of specificity metrics to support tasks such as SNP detection, scaffolding of draft assemblies, comparative genomics, and metagenomic analyses.

Key Features:

• Fast kmer profile-based lookup: Quickly identifies candidate reference genomes (CRGs) from high-quality databases using kmer profiles.
• Specificity metrics: Computes mutual highly specific ANI and conserved DNA values to evaluate and rank candidate reference genomes.
• Database sources: Uses high-quality databases such as NCBI RefSeq for candidate identification.
• Integration and scalability: Provides an integrated workflow designed to handle large genomic datasets efficiently.
• Optimized for speed: Implements rapid computation steps to reduce time required for reference genome selection.

Scientific Applications:

• SNP detection: Selection of reference genomes to improve accuracy of single nucleotide polymorphism identification.
• Scaffolding of draft assemblies: Identification of suitable references to guide scaffolding and assembly improvement.
• Comparative genomics: Choice of reference genomes for genome-to-genome comparisons and phylogenomic analyses.
• Metagenomic analyses: Reference selection for taxonomic and functional profiling in metagenomic datasets.

Methodology:

Performs kmer profile-based lookup against high-quality databases (e.g., NCBI RefSeq) to identify CRGs, then computes mutual highly specific ANI and conserved DNA values; references and leverages similarity estimation methods such as ANI calculations, DNA–DNA hybridization approaches, and Mash (MinHash-based) for distance estimation.