GABOLA

GABOLA integrates linked short reads and long reads to improve genome assembly by filling intra- and inter-scaffold gaps and resolving complex genomic regions for applications in precision medicine and genome breeding.

Key Features:

• Integration of long-range genomic information: Combines accurate linked short reads (such as 10x Genomics) with long reads to increase assembly integrity and resolution.
• Gap-filling capabilities: Fills intra- and inter-scaffold gaps to achieve more complete and contiguous assemblies, including recovery of sequences spanning millions of base pairs.
• Compatibility with sequencing technologies: Operates with linked reads, third-generation sequencing (TGS) long reads, and other gap-filling techniques for versatile application.
• Repeat and variant discovery: Uncovers extensive repeat sequences and exclusive sequence patterns and facilitates recovery of exons and transcripts relevant to cancer and other disorders.

Scientific Applications:

• Precision Medicine: Enhances identification of functional genes and variants by filling large gaps and recovering thousands of exons and transcripts in human genomes related to cancer and other disorders.
• Genome Breeding: Improves assembly completeness and raises genetic benchmarking scores in non-model organisms (e.g., Japanese eel), adding genomic content useful for breeding programs and evolutionary studies.
• Repeat-sequence analysis: Enables discovery of extensive repeat sequences and exclusive patterns linked to disorders, including neurodegenerative diseases.

Methodology:

Integrates long-range genomic information from linked short reads (e.g., 10x Genomics) and long reads to resolve complex genomic regions and fill intra- and inter-scaffold gaps; validated on human and Japanese eel genomes.