StriDe

StriDe integrates string and de Bruijn graph models to assemble genomes with improved contiguity and accuracy across short-read and long-read datasets.

Key Features:

• Adaptive Decomposition: Decomposes reads selectively within error-prone regions to leverage string-graph resolution of repeats while minimizing loss of sequence data.
• Extension of Paired-End Reads: Extends paired-end reads into longer contiguous sequences using an FM-index to bridge gaps across complex and repetitive regions.
• Assembly Graph Construction: Constructs an assembly graph by combining decomposed and extended reads to improve repeat resolution and genome reconstruction accuracy.
• Parallelization and Optimization: Implements full parallelization and optimized components for scalable processing of large sequencing datasets.

Scientific Applications:

• Complex Genome Assembly: Assembles genomes with repetitive regions and sequencing errors to produce higher-contiguity reference sequences.
• Comparative Genomics: Generates high-quality assemblies suitable for comparative analyses across species or strains.
• Clinical Genomics: Produces accurate and contiguous assemblies applicable to clinical genomics workflows requiring precise genomic information.

Methodology:

Combines string graph and de Bruijn graph techniques, selectively decomposes reads in error-prone regions, extends paired-end reads using an FM-index, constructs an assembly graph from decomposed and extended reads, and employs full parallelization and component optimizations.