A Robust and Efficient DNA Storage Architecture Based on Modulation Encoding and Decoding

Synthetic DNA has been widely considered an attractivemedium fordigital data storage. However, the random insertion-deletion-substitution(IDS) errors in the sequenced reads still remain a critical challengeto reliable data recovery. Motivated by the modulation technique inthe communication field, we propose a new DNA storage architectureto solve this problem. The main idea is that all binary data are modulatedinto DNA sequences with the same AT/GC patterns, which facilitatethe detection of indels in noisy reads. The modulation signal couldnot only satisfy the encoding constraints but also serve as priorinformation to detect the potential positions of errors. Experimentson simulation and real data sets demonstrate that modulation encodingprovides a simple way to comply with biological constraints for sequenceencoding (i.e., balanced GC content and avoiding homopolymers). Furthermore,modulation decoding is highly efficient and extremely robust, whichcan correct up to & SIM;40% of errors. In addition, it is robustto imperfect clustering reconstruction, which is very common in practice.Although our method has a relatively low logical density of 1.0 bits/nt,its high robustness may provide a wide space for developing low-costsynthetic technologies. We believe this new architecture may boostthe early coming of large-scale DNA storage applications in the future.

Automated summary

Synthetic DNA is considered as a potential medium for digital data storage, but the errors in read sequences remain a challenge. Inspired by modulation techniques, a new DNA storage architecture is proposed to modulate binary data into DNA sequences with the same AT/GC patterns, making it easier to detect errors. Experiments show that modulation encoding complies with biological constraints and can correct up to 40% of errors.