RepairNatrix

RepairNatrix performs constraint-aware preprocessing and heuristic repair of raw sequencing data for DNA storage, leveraging prior information from error-correcting and constrained codes to improve decoding and data recoverability.

Key Features:

• Preprocessing Capabilities: Preprocesses raw sequencing data to prepare it for error correction and decoding in DNA storage pipelines.
• Constraint Utilization: Incorporates constraints from constrained codes as prior information to enforce structural rules during processing.
• Error Correction and Repair: Implements heuristic algorithms to flag and repair sequences that violate imposed constraints, increasing recoverability of encoded data.
• Efficiency Improvements: Reduces the number of raw reads required for error-free decoding by a factor of 25–35 across evaluated datasets.
• Reproducibility and Fair Comparisons: Provides a tailored workflow for comparing DNA storage codes and producing reproducible benchmarking results.

Scientific Applications:

• DNA storage preprocessing: Prepares raw sequencing reads for downstream error-correction and decoding of DNA-encoded files.
• Error recovery enhancement: Enhances recovery of encoded data by combining constraint information with heuristic repairs to reduce decoding failures.
• Benchmarking and evaluation: Enables fair, reproducible comparisons between error-correcting and constrained code implementations in DNA storage research.

Methodology:

Integrates constraint-based preprocessing with heuristic repair mechanisms that leverage prior constraint information to flag and correct sequences violating constraints.