ReLume: Enhancing DNA storage data reconstruction with flow network and graph partitioning

IF 4.2 3区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Methods Pub Date : 2025-04-21 DOI:10.1016/j.ymeth.2025.03.022

Lei Xie , Ben Cao , Xiaoru Wen , Yanfen Zheng , Bin Wang , Shihua Zhou , Pan Zheng

引用次数: 0

Abstract

DNA storage is an ideal alternative to silicon-based storage, but focusing on data writing alone cannot address the inevitable errors and durability issues. Therefore, we propose ReLume, a DNA storage data reconstruction method based on flow networks and graph partitioning technology, which can accomplish the data reconstruction task of millions of reads on a laptop with 24 GB RAM. The results show that ReLume copes well with many types of errors, more than doubles sequence recovery rates, and reduces memory usage by about 60 %. ReLume is 10 times more durable than other representative methods, meaning that data can be read without loss after 100 years. Results from the wet lab DNA storage dataset show that ReLume’s sequence recovery rates of 73 % and 93.2 %, respectively, significantly outperform existing methods. In summary, ReLume effectively overcomes the accuracy and hardware limitations and provides a feasible idea for the portability of DNA storage.

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reume：利用流网络和图分区增强DNA存储数据重构

DNA存储是硅基存储的理想替代品，但仅关注数据写入无法解决不可避免的错误和耐久性问题。因此，我们提出了一种基于流网络和图分区技术的DNA存储数据重构方法——ReLume，它可以在一台24gb RAM的笔记本电脑上完成数百万次读取的数据重构任务。结果表明，reume可以很好地处理多种类型的错误，序列恢复率提高了一倍以上，并将内存使用减少了约60%。reume的耐用性是其他代表性方法的10倍，即可以在100年后读取数据而不丢失。来自湿实验室DNA存储数据集的结果表明，ReLume的序列回收率分别为73%和93.2%，显著优于现有方法。总之，ReLume有效地克服了准确性和硬件限制，为DNA存储的可移植性提供了可行的思路。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Methods 生物-生化研究方法

CiteScore

9.80

自引率

2.10%

发文量

222

审稿时长

11.3 weeks

期刊介绍： Methods focuses on rapidly developing techniques in the experimental biological and medical sciences. Each topical issue, organized by a guest editor who is an expert in the area covered, consists solely of invited quality articles by specialist authors, many of them reviews. Issues are devoted to specific technical approaches with emphasis on clear detailed descriptions of protocols that allow them to be reproduced easily. The background information provided enables researchers to understand the principles underlying the methods; other helpful sections include comparisons of alternative methods giving the advantages and disadvantages of particular methods, guidance on avoiding potential pitfalls, and suggestions for troubleshooting.