Ragout

Ragout assembles bacterial genomes from high-throughput short-read sequencing assemblies by ordering and scaffolding contigs using multiple complete reference genomes and their evolutionary relationships to improve scaffold continuity.

Key Features:

• Multiple Reference Utilization: Employs multiple complete reference genomes and incorporates their evolutionary relationships via a phylogenetic tree to determine contig order.
• Genome Rearrangement Strategy: Applies genome rearrangement approaches to model structural differences among references and guide the ordering and assembly of contigs into scaffolds.
• Assembly Graph and Multi-Scale Synteny Blocks: Integrates the input assembly graph with multi-scale synteny blocks to address gaps caused by small contigs and to reduce assembly errors.
• Alternative to Long-Read Technologies: Provides a reference-based scaffolding alternative to long reads such as Pacific Biosciences (PacBio) or jumping libraries by leveraging existing complete genomes of related strains.

Scientific Applications:

• Improved bacterial genome assembly: Enhances draft assemblies from short-read sequencing for bacterial species with multiple related complete genomes, and in simulations and real datasets can yield a single high-quality scaffold per chromosome.

Methodology:

Uses multiple reference genomes and their phylogenetic relationships, applies genome rearrangement algorithms to order and scaffold contigs, and integrates the assembly graph with multi-scale synteny blocks to bridge gaps and reduce errors.