Dna sequence reconstruction improves with cross-cluster context guidance
CCP-DP: Cross-cluster context-guided phase dynamic programming for DNA storage sequence reconstruction
Information Retrieval
Summary
Reading information stored in DNA is tricky because errors like extra or missing pieces make it hard to know the exact sequence. Existing methods mostly rely on clues within small groups of DNA reads, which can fail when there isn’t enough data or when errors cause shifts in the sequence. The authors present a new method called CCP-DP that looks across different groups of DNA reads to get a clearer picture and fix uncertain parts. This approach improves how accurately DNA sequences can be reconstructed, especially when the data is limited or noisy.
What this means in practice
- •For dna storage engineers: Reconstruct stored DNA sequences more accurately at low sequencing coverage using cross-cluster information.
- •For error correction system developers: Integrate cross-cluster context into sequencing error correction pipelines to improve handling of indel-caused phase shifts.
Authors
Zixin Zhang, Guanjin Qu, Huaming Wu
Abstract
Motivation: DNA data storage offers high information density and long-term stability, but accurate sequence reconstruction remains challenging under limited sequencing coverage and strong insertion, deletion, and substitution (IDS) noise. Existing reconstruction methods mainly rely on local evidence within individual read clusters. When sequencing coverage is low or indel-induced phase shifts become pronounced, such local evidence may be insufficient to distinguish closely competing candidate sequences. Results: We present Cross-Cluster Context-Guided Phase Dynamic Programming (CCP-DP), which uses dataset-level cross-cluster information to complement cluster-local evidence and selectively refines ambiguous provisional consensuses. Under the main benchmark settings, CCP-DP achieved exact reconstruction rates of 95.36%-99.98% and outperformed existing methods on multiple datasets. At $5\times$ coverage, CCP-DP improved exact reconstruction by 6.2-17.5 percentage points over the stronger of BBS and CPL across the tested IDS conditions, while maintaining low reconstruction error and computational overhead. Overall, CCP-DP introduces cross-cluster shared information as a complementary source of evidence for DNA sequence reconstruction under challenging conditions. Availability: Source code is available at https://github.com/ZixinZ3899/CCP-DP.