PAFScaff

PAFScaff maps genome assembly scaffolds onto a closely-related chromosome-level reference genome to anchor scaffolds and perform super-scaffolding for improved assembly contiguity and accuracy.

Key Features:

• Reference-Based Mapping: Uses Minimap2 to perform all-against-all mappings between assembly scaffolds and a reference genome, producing PAF (Pairwise mApping Format) output.
• PAF Parsing and Assignment: Parses PAF mappings to assign assembly scaffolds to specific reference chromosomes based on alignment results.
• Super-Scaffolding: Links multiple scaffolds into super-scaffolds by inferring relative scaffold order and orientation from reference-alignment positions.

Scientific Applications:

• Reference-guided scaffolding: Improves scaffold placement and orientation when a high-quality chromosome-level reference is available.
• Assembly improvement for downstream analyses: Enhances contiguity and accuracy of assemblies used for variant calling and comparative genomics.
• Applied genome projects: Has been applied in genome assembly projects such as the Nala German Shepherd Dog assembly to improve assembly contiguity.

Methodology:

Performs all-against-all mapping with Minimap2 to produce PAF output, parses PAF alignments to assign scaffolds to reference chromosomes, and links scaffolds into super-scaffolds based on inferred relative positions and orientations from the reference alignments.