CONTIGuator

CONTIGuator maps draft genome contigs onto reference and complete-genome templates to assist bacterial genome finishing and comparative structural genomics.

Key Features:

• Contig Mapping: Maps contigs over a reference genome and produces detailed genomic maps to identify contig positions and assist gap closure.
• Handling Multipartite Genomes: Manages genomes with multiple replicons, including multiple circular chromosomes and plasmids, for accurate finishing of multipartite bacterial genomes.
• Visualization of Genetic Elements: Generates maps highlighting loss and gain of genetic elements to aid detection of structural variations and genomic rearrangements.
• Template-based Mapping: Leverages complete genomes as templates to guide contig placement and comparative structural analysis.
• Implementation: Implemented as a Python-based script optimized for Linux environments.
• Validation: Tested on four diverse bacterial genomes with reported superior performance compared to existing solutions.

Scientific Applications:

• Comparative Structural Genomics: Enables comparison of draft genomes against complete templates to study genome architecture and structural differences.
• Bacterial Genome Finishing: Facilitates closure of sequencing gaps and ordering of contigs to achieve more complete bacterial genome assemblies, including multipartite genomes.
• Detection of Structural Variation: Supports identification and visualization of gains, losses, and rearrangements of genetic elements.

Methodology:

CONTIGuator uses a Python-based script on Linux to map contigs onto complete-genome templates and generate genomic maps showing contig positions and loss/gain of genetic elements.