Post Assembly Genome Improvement Toolkit

Post Assembly Genome Improvement Toolkit improves draft genome assemblies by closing gaps, correcting consensus base errors, leveraging reference genomes for improved scaffolding and annotation, and generating gene model annotations for bacterial and small eukaryotic genomes up to 300 megabases (Mb) from high-throughput sequencing.

Key Features:

• Gap Closure: Efficiently closes gaps within scaffolds to increase sequence contiguity.
• Error Correction: Corrects consensus base errors to improve sequence accuracy.
• Reference Genome Utilization: Uses available reference genomes to guide scaffolding and improve annotation quality via comparative approaches.
• Annotation Generation: Produces gene model annotations to provide functional information for assembled genomes.

Scientific Applications:

• Pathogenic bacterial genomics: Improves draft assemblies for pathogenic bacteria to support downstream comparative and functional analyses.
• Parasitic eukaryote genomics: Refines assemblies of malaria parasites (Plasmodium) and parasitic worms to aid parasitology and genomics studies.
• Benchmarking and rapid finishing: Demonstrated improvement of an Escherichia coli assembly in approximately 24 hours, indicating applicability for rapid genome finishing.

Methodology:

The protocol employs automated steps including gap closure, consensus base error correction, reference-guided scaffolding, and gene model annotation; reported outcomes include approximately doubling the average contig size and annotating over 4,300 gene models.