NextDenovo

NextDenovo performs de novo genome assembly from long-read sequencing data (PacBio CLR, PacBio HiFi, and Oxford Nanopore Technologies) to reconstruct genomes for downstream analyses such as structural variation and copy-number investigation.

Key Features:

• String Graph-Based Assembly: Uses string graph algorithms to assemble long reads into contiguous sequences.
• Correct-then-Assemble Strategy: Employs a "correct-then-assemble" workflow similar to Canu for handling noisy long reads.
• Error Correction: Implements an error correction mechanism optimized for high-error-rate data such as ONT reads and skips the correction step for PacBio HiFi reads.
• Sequencing Technology Support: Supports PacBio CLR, PacBio HiFi, and Oxford Nanopore Technologies long-read data.
• Resource Efficiency: Optimized to reduce computational resource usage and storage requirements compared to similar assemblers.

Scientific Applications:

• Human genome assembly: Has been applied to assemble 35 diverse human genomes using Oxford Nanopore Technologies long-read data.
• Structural variation and duplication analysis: Enables identification of segmental duplications and gene copy-number variations.
• Population-scale assembly: Facilitates population-scale genome assembly projects using long-read sequencing data.

Methodology:

NextDenovo applies a "correct-then-assemble" strategy using string graph algorithms with error correction for noisy reads while skipping correction for PacBio HiFi reads and is optimized to reduce computational resource and storage requirements.