ntJoin

ntJoin leverages structural synteny between draft and reference assemblies to scaffold and improve genome assembly contiguity and overall assembly quality.

Key Features:

• Assembly Scaffolding: Scaffolds a target draft assembly using one or more reference assemblies, which can be true reference builds or alternative draft genomes.
• Lightweight Mapping Approach: Employs a mapping strategy based on minimizer graphs generated from ordered minimizer sketches, avoiding traditional alignment methods to reduce runtime and memory usage.
• Versatility in Applications: Applicable to enhancing draft assemblies with reference-grade genomes, integrating short read assemblies with long read drafts, or using assemblies from closely related species for scaffolding.

Scientific Applications:

• Improvement of Genome Assemblies: Enhances assembly contiguity; for example, scaffolding a human short read assembly with either the human reference genome or a long read assembly increased NGA50 length by 23-fold and 13-fold, respectively.
• Resource Efficiency: Performs scaffolding in under 13 minutes using less than 11 GB of RAM, demonstrating lower runtime and memory compared with existing reference-guided assemblers.

Methodology:

Requires a target assembly and one or more reference assemblies as input; utilizes minimizer graphs derived from ordered minimizer sketches to map and scaffold the target relative to the references while avoiding traditional alignment methods.