CHERIPIC

CHERIPIC identifies homozygosity-enriched genomic regions from bulk segregant sequencing data to prioritize candidate causative variants in fragmented or un-scaffolded draft genomes.

Key Features:

• Name and approach: Computes Homozygosity Enriched Regions In genomes to Prioritise Identification of Candidate variants (CHERIPIC) as its core conceptual framework.
• Bulk segregant analysis: Analyzes bulk segregant sequencing data to detect genomic regions associated with the segregating phenotype.
• Homozygosity enrichment detection: Identifies regions enriched for homozygosity that are indicative of potential causative mutations.
• Draft genome compatibility: Operates on fragmented or un-scaffolded draft genome assemblies without requiring an ordered reference genome.
• Candidate prioritization: Ranks and narrows candidate causative variants based on patterns of homozygosity enrichment.

Scientific Applications:

• Mutation mapping from bulk segregant data: Prioritizes candidate causative mutations underlying segregating phenotypes using bulk segregant sequencing.
• Cross-species genomic analysis: Validated on bulk segregant sequence data from Arabidopsis, maize, and barley, demonstrating applicability across diverse plant genomes.

Methodology:

Analyzes bulk segregant sequence data to identify regions enriched for homozygosity and prioritize candidate variants.