NECAT

NECAT performs error correction and de novo genome assembly of long nanopore sequencing reads to improve read accuracy and assembly contiguity for downstream genomic analyses such as structural variation detection.

Key Features:

• Nanopore long-read support: Designed specifically for long nanopore sequencing reads and their characteristic error profiles.
• Adaptive read selection: Implements adaptive read selection to prioritize reads for error correction and assembly.
• Two-step progressive error correction: Uses a two-step progressive method for rapid and precise error correction while maintaining read length.
• Two-stage assembler: Employs a two-stage (dual-phase) assembler to leverage extended read lengths and improve assembly quality and continuity.
• Preserves read length: Avoids trimming high-error-rate subsequences during correction to preserve read length and assembly contiguity.
• Error handling: Explicitly addresses broad distributions of errors and high-error-rate subsequences characteristic of nanopore reads.
• Assembly contiguity improvement: Demonstrated a 2.47-fold improvement in NG50 on a 35X human genome assembly that completed in 8,122 hours.
• High-quality assembly example: Achieved an NG50 of 22 Mbp on the human WERI cell line.
• Improved structural-variation reliability: Reduces false positives in structural variation detection by improving assembly accuracy and continuity.

Scientific Applications:

• De novo genome assembly: Assembly of complex genomes from long nanopore reads to increase contiguity and completeness.
• Structural variation analysis: Supports structural variation detection by providing higher-accuracy, more contiguous assemblies that reduce false positives.
• Human genome assembly and benchmarking: Applied to human datasets including a 35X human genome assembly and the WERI cell line (NG50 22 Mbp).

Methodology:

Adaptive read selection, a two-step progressive error-correction procedure, and a two-stage (dual-phase) assembler are employed.