KCFtools

KCFtools identifies the presence and absence of k-mers in non-overlapping genomic or transcriptomic windows by comparing query and reference genomes, enabling alignment-free introgression screening and GWAS using k-mer profiles.

Key Features:

• Alignment-free k-mer profiling: Identifies the presence and absence of k-mers in non-overlapping genomic or transcriptomic windows without read alignment.
• Identity score computation: Computes an identity score for each window to facilitate robust detection of introgressed or variable regions across genomes.
• Genotype matrix generation: Generates genotype matrices from k-mer variation tables that are compatible with Genome-Wide Association Studies (GWAS) software.
• Reference-agnostic analysis: Captures introgressed segments and structurally diverse regions even in species with fragmented or highly divergent reference genomes.

Scientific Applications:

• Introgression detection: Detects introgressed segments and highly variable genomic regions in large-genome crop species such as lettuce or wheat.
• Genome-Wide Association Studies: Identifies loci associated with phenotypic traits, as demonstrated by detecting known and novel associations for downy mildew resistance in lettuce.
• Population genetic analysis: Enables high-resolution, reference-agnostic population genetic analysis across multiple genome references.

Methodology:

KCFtools compares query and reference genomes to identify the presence and absence of k-mers in non-overlapping genomic or transcriptomic windows, computes an identity score for each window, and generates genotype matrices from k-mer variation tables for downstream GWAS analysis.