Redundans

Redundans: Heterozygous Genome Assembly Refinement and Scaffolding Pipeline

Redundans refines and scaffolds genome assemblies of heterozygous organisms by identifying and removing alternative heterozygous contigs, reducing redundancy, fragmentation, and assembly size inflation.

Key Features:

• Alternative Contig Reduction: Identifies and selectively removes alternative heterozygous contigs to resolve multiple assembly paths between homozygous and heterozygous regions.
• Scaffolding and Gap Closure: Scaffolds input contigs using sequencing libraries and/or reference sequences and automatically closes gaps from initial assembly or scaffolding steps.
• Assembly Size Optimization: Produces assemblies with total size smaller than the sum of input contigs by eliminating redundant haplotypic sequences.

Scientific Applications:

• Heterozygous Genome Assembly: Improves assembly continuity and accuracy in simulated and naturally occurring heterozygous genomes, including hybrid organisms and species with high genetic diversity.
• Downstream Genomic Analysis: Reduces errors in gene models, gene copy number estimation, and synteny analysis.

Methodology:

Redundans accepts assembled contigs, sequencing libraries, and/or reference sequences as input. It distinguishes homozygous and heterozygous regions, removes alternative heterozygous contigs to resolve redundant assembly paths, scaffolds contigs to reduce fragmentation, and closes assembly gaps to improve structural continuity and annotation accuracy.