BRIDGEcereal

BRIDGEcereal accelerates large-indel discovery and structural haplotype visualization across pan-genome de novo assemblies of major cereal crops to support comparative genomics and candidate gene prioritization.

Key Features:

• Unsupervised machine learning: Two unsupervised modules perform comparative structural analyses across multiple assemblies.
• CHOICE: CHOICE (clustering HSPs for ortholog identification via coordinates and equivalence) extracts orthologous gene segments using high-scoring segment pairs (HSPs) as anchors.
• CLIPS: CLIPS (clustering via large-indel permuted slopes) clusters extracted segments by shared large-indel patterns to derive concise haplotype groupings.
• Large-indel detection: Targets large insertions and deletions that are difficult to characterize by short-read alignment against a single reference.
• Indel-level outputs: Reports indel locations, sizes, and inferred relationships among haplotypes for comparative interpretation.
• Search-window and ordering refinement: Supports iterative refinement of upstream/downstream search windows and haplotype ordering for intergenic indels with uncertain boundaries.
• Pan-genome scale: Integrates 120 assemblies from wheat, barley, maize, sorghum, and rice, including complex polyploid genomes.

Scientific Applications:

• QTL and GWAS mapping: Mapping structural haplotypes in QTL and GWAS intervals in wheat to link structural variation to phenotypic variation.
• Structural variant interpretation: Interpreting large indels that reshape gene structure and modulate expression in crop genomes.
• Comparative genomics: Comparative analysis of pan-genome assemblies across wheat, barley, maize, sorghum, and rice.
• Candidate gene discovery: Prioritizing candidate causal genes by associating structural haplotypes with phenotypic signals.

Methodology:

Two unsupervised machine learning modules are applied: CHOICE extracts orthologous segments from multiple de novo assemblies using HSPs as anchors, and CLIPS clusters those segments by shared indel patterns to derive haplotype groupings.