Multi-CSAR

Multi-CSAR integrates multiple reference genomes to scaffold a target genome, improving assembly continuity and enabling comparative genomic analyses.

Key Features:

• Multiple Reference Integration: Integrates information from multiple reference genomes to inform scaffold structure for a single target genome.
• Sequence Marker Identification: Identifies sequence markers shared between the target and each reference genome to support contig alignment within scaffolds.
• Scaffold Computation: Computes scaffolds from each reference genome individually and merges them into a comprehensive scaffold derived from all references.
• Input Formats: Accepts target and one or more reference genomes in multi-FASTA format.
• Reference Weighting Scheme: Applies a weighting scheme that assigns different weights to reference genomes to adjust their influence on the final scaffold.
• Marker Detection Modes: Supports marker identification using NUCmer on nucleotide sequences or PROmer on translated amino acids.

Scientific Applications:

• Complex genome assembly: Improves scaffolding for genomes with repetitive regions by leveraging multiple references.
• Comparative genomics: Enables integration of diverse reference datasets for comparative analyses across genomes.
• Evolutionary biology: Facilitates reconstruction of genome structure for evolutionary inference using multiple reference frameworks.
• High-precision scaffolding: Supports projects requiring precise scaffold construction through combined reference evidence.

Methodology:

Identifies shared sequence markers between the target and each reference using NUCmer (nucleotide) or PROmer (translated amino acids), aligns contigs within scaffolds based on those markers, computes scaffolds per reference and combines them using a weighting scheme, and provides outputs as Circos plots, dotplots, and detailed tables.