ArticleBMC bioinformatics2022
DeSP: a systematic DNA storage error simulation pipeline.
Article in BMC bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 20 citations in OpenAlex.
- Polus: a context-aware enhancement framework for DNA storage via transformer-based soft-decision decoding.Bioinformatics (Oxford, England) · 2026Article
- From spacecraft ranging to massive DNA data storage: Composite ranging codes as indices and error correction references.Science advances · 2026Article
- Approaching single-molecule assembly-free readout from medium-length encoded DNA.Nature communications · 2025Article
- DNA-CTMF: Reconstruct high quality image from lossy DNA storage via Pixel-Base codebook and median filter.Synthetic and systems biotechnology · 2025Article
- Dna-storalator: a computational simulator for DNA data storage.BMC bioinformatics · 2025Article
- A generative adversarial network for multiple reads reconstruction in DNA storage.Scientific reports · 2024Article
- DNA Bloom Filter enables anti-contamination and file version control for DNA-based data storage.Briefings in bioinformatics · 2024Article
- FrameD: framework for DNA-based data storage design, verification, and validation.Bioinformatics (Oxford, England) · 2023Article
- A digital twin for DNA data storage based on comprehensive quantification of errors and biases.Nature communications · 2023Article
- Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage.BMC bioinformatics · 2023Article
- Correction to: DeSP: a systematic DNA storage error simulation pipeline.BMC bioinformatics · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
Abstract
backgroundUsing DNA as a storage medium is appealing due to the information density and longevity of DNA, especially in the era of data explosion. A significant challenge in the DNA data storage area is to deal with the noises introduced in the channel and control the trade-off between the redundancy of error correction codes and the information storage density. As running DNA data storage experiments in vitro is still expensive and time-consuming, a simulation model is needed to systematically optimize the redundancy to combat the channel's particular noise structure.
resultsHere, we present DeSP, a systematic DNA storage error Simulation Pipeline, which simulates the errors generated from all DNA storage stages and systematically guides the optimization of encoding redundancy. It covers both the sequence lost and the within-sequence errors in the particular context of the data storage channel. With this model, we explained how errors are generated and passed through different stages to form final sequencing results, analyzed the influence of error rate and sampling depth to final error rates, and demonstrated how to systemically optimize redundancy design in silico with the simulation model. These error simulation results are consistent with the in vitro experiments.
conclusionsDeSP implemented in Python is freely available on Github ( https://github.com/WangLabTHU/DeSP ). It is a flexible framework for systematic error simulation in DNA storage and can be adapted to a wide range of experiment pipelines.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.