ArticlePloS one2017
DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
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- Effects of Indoor Air Purifiers on Children with Asthma.Yonsei medical journal · 2020Trial
- Rhizosphere and endophytic bacterial communities of the endangered alpine modest primrose and their plant growth-promoting potential.Scientific reports · 2026Article
- Longitudinal remodeling of gastric microbiota followingFrontiers in cellular and infection microbiology · 2026Article
- Native Rhizobial Inoculation Improves Tomato Yield and Nutrient Uptake While Mitigating Heavy Metal Accumulation in a Conventional Farming System.Microorganisms · 2025Article
- Comparative metagenomic analysis of 16S RNA amplicon sequencing of bacterial population of an industrial site contaminated with halogenated anilines.Microbiology resource announcements · 2025Article
- Functional profiling of the oral microbiome reveals microbial and oncogenic signatures in never-smoking female patients with oral squamous cell carcinoma.Journal of oral microbiology · 2025Article
- The Possible Preventative Role of Lactate- and Butyrate-Producing Bacteria in Colorectal Carcinogenesis.Gut and liver · 2024Article
- From colon wall to tumor niche: Unraveling the microbiome's role in colorectal cancer progression.PloS one · 2024Article
- Comprehensive analysis of the microbiome inPeerJ · 2024Article
- Changes in Gut Microbiome upon Orchiectomy and Testosterone Administration in AOM/DSS-Induced Colon Cancer Mouse Model.Cancer research and treatment · 2023Article
- Characteristics of rhizosphere and endogenous bacterial community of Ulleung-sanmaneul, an endemic plant in Korea: application for alleviating salt stress.Scientific reports · 2022Article
- The Gut Microbiota at Different Developmental Stages ofMicroorganisms · 2022Article
- Effect of luxS encoding a synthase of quorum-sensing signal molecule AI-2 of Vibrio vulnificus on mouse gut microbiome.Applied microbiology and biotechnology · 2022Article
- Influence ofJournal of ginseng research · 2022Article
- MicroSEC filters sequence errors for formalin-fixed and paraffin-embedded samples.Communications biology · 2021Article
- Analysis of the Conjunctival Microbiome in Patients with Atopic Keratoconjunctivitis and Healthy Individuals.Annals of dermatology · 2021Article
- Compositional and Functional Changes in the Gut Microbiota in Irritable Bowel Syndrome Patients.Gut and liver · 2021Article
- Changes in Microbial Community Composition Related to Sex and Colon Cancer by Nrf2 Knockout.Frontiers in cellular and infection microbiology · 2021Article
- Features of Bacterial Microbiota in the Wild Habitat ofFrontiers in microbiology · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We consider the correction of errors from nucleotide sequences produced by next-generation targeted amplicon sequencing. The next-generation sequencing (NGS) platforms can provide a great deal of sequencing data thanks to their high throughput, but the associated error rates often tend to be high. Denoising in high-throughput sequencing has thus become a crucial process for boosting the reliability of downstream analyses. Our methodology, named DUDE-Seq, is derived from a general setting of reconstructing finite-valued source data corrupted by a discrete memoryless channel and effectively corrects substitution and homopolymer indel errors, the two major types of sequencing errors in most high-throughput targeted amplicon sequencing platforms. Our experimental studies with real and simulated datasets suggest that the proposed DUDE-Seq not only outperforms existing alternatives in terms of error-correction capability and time efficiency, but also boosts the reliability of downstream analyses. Further, the flexibility of DUDE-Seq enables its robust application to different sequencing platforms and analysis pipelines by simple updates of the noise model. DUDE-Seq is available at http://data.snu.ac.kr/pub/dude-seq.
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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.