RaGOO

RaGOO performs reference-guided scaffolding of draft genome assemblies by ordering and orienting contigs into chromosome-scale pseudomolecules using Minimap2 alignments to a closely related reference genome.

Key Features:

• Speed and Sensitivity: Leverages Minimap2 alignments to rapidly process contigs and sensitively detect alignment relationships.
• Reference-Guided Scaffolding: Orders and orients contigs against a reference genome to produce chromosome-scale pseudomolecules.
• Structural Variant Detection: Identifies structural variants, including those spanning sequencing gaps, from contig-to-reference alignments.
• Scalability: Applicable to large datasets, demonstrated by assembly of 103 Arabidopsis thaliana accessions for pan-genome analysis.

Scientific Applications:

• Tomato genome assembly: Ordering and orienting de novo tomato genome assemblies, including the M82 cultivar, into chromosome-scale pseudomolecules.
• Structural variant analysis: Detection and characterization of structural variants in newly assembled pseudomolecules.
• Pan-genome analyses: Large-scale assembly and comparison across Arabidopsis thaliana accessions.

Methodology:

Aligns contigs to a reference genome using Minimap2 to order and orient them into pseudomolecules and to identify structural variants, including those spanning sequencing gaps.