CG-CAT

CG-CAT predicts adjacency, order, and orientation of genomic contigs by integrating sequence similarity and phylogenetic information from related genomes to support genome assembly finishing.

Key Features:

• Phylogeny-Aware Contig Adjacency Prediction: Estimates the likelihood of adjacency between contigs using both sequence similarity and phylogenetic relationships among related genomes.
• Graph-Based Layout Construction: Builds a layout graph representing potential contig adjacencies and alternative genome arrangements.
• Comparative Assembly Support: Utilizes genomic information from related species or strains to guide contig ordering and orientation.
• Synteny Visualization: Enables inspection of conserved gene order across genomes to support interpretation of contig arrangements.

Scientific Applications:

• Genome Assembly Finishing: Assists in ordering and orienting contigs during the final stages of genome assembly.
• Comparative Genomics: Investigates genome organization and synteny among related organisms using comparative assembly approaches.

Methodology:

CG-CAT constructs a graph of candidate contig adjacencies derived from sequence similarity and phylogenetic relationships and generates layout graphs to infer likely contig order and orientation.