ragtag

RagTag: Reference-guided genome scaffolding and assembly refinement suite

RagTag performs reference-guided scaffolding and enhancement of genome assemblies. Its component RaGOO orders and orients contigs using Minimap2 alignments to construct chromosome-scale pseudomolecules and improve assembly accuracy and completeness.

Key Features:

• Reference-guided scaffolding: Orders and orients contigs against a reference genome to generate chromosome-scale assemblies.
• Pseudomolecule construction: Builds contiguous sequences approximating full chromosomes from assembled contigs.
• Structural variant detection: Identifies structural variants, including variants spanning sequencing gaps, after assembly.
• Minimap2 integration: Leverages Minimap2 for rapid and sensitive sequence alignment during contig placement.

Scientific Applications:

• De novo genome assembly refinement: Applied to tomato (M82 reference cultivar) assemblies for accurate contig ordering and orientation.
• Pan-genome structural variation analysis: Detected structural variants across 103 Arabidopsis thaliana accessions using newly assembled pseudomolecules.

Methodology:

RaGOO aligns assembled contigs to a reference genome using Minimap2, clusters and orders contigs by alignment coordinates, orients them to match the reference, and concatenates them into chromosome-scale pseudomolecules. Post-scaffolding, it analyzes alignments to identify structural variants, including those spanning sequencing gaps.