SibeliaZ

SibeliaZ identifies and reconstructs locally collinear blocks for multiple whole-genome alignment using compacted de Bruijn graphs.

Key Features:

• Scalability: Implements the SibeliaZ-LCB algorithm and leverages compacted de Bruijn graph analysis to identify collinear blocks across many and long assembled genomes.
• Efficiency: Demonstrates reduced runtime versus existing methods, completing alignment of sixteen recently assembled strains of mice in under 16 hours on a single machine while other tools failed to finish alignments for eight mice within a week.
• Accuracy: Maintains high alignment and collinear block reconstruction accuracy for closely related genomes.
• Output Formats: Reports locally collinear block coordinates in GFF format and provides alignments in MAF format.

Scientific Applications:

• Comparative genomics: Aligns multiple genomes to detect genetic variation and conserved genomic regions across species.
• Evolutionary biology: Supports analysis aimed at understanding evolutionary relationships among closely related genomes.
• Functional genomics: Assists identification of conserved regions that may be associated with functional genomic elements.

Methodology:

Uses compacted de Bruijn graphs to identify anchors that the SibeliaZ-LCB algorithm extends into locally collinear blocks.