ArticleGenome biology2016
Streamlined analysis of duplex sequencing data with Du Novo.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed.
- Benchmarking UMI clustering tools for accurate detection of low-frequency variants from deep sequencing.Scientific reports · 2025Article
- Alignment-free unique molecular identifier clustering suppresses sequencing errors for accurate detection of low-frequency DNA variants.Briefings in bioinformatics · 2025Article
- Allele frequency selection and no age-related increase in human oocyte mitochondrial mutations.Science advances · 2025Article
- A side-by-side comparison of variant function measurements using deep mutational scanning and base editing.Nucleic acids research · 2025Article
- Sequencing by binding rivals SMOR error-corrected sequencing by synthesis technology for accurate detection and quantification of minor (< 0.1%) subpopulation variants.BMC genomics · 2024Article
- Leveraging new methods for comprehensive characterization of mitochondrial DNA in esophageal squamous cell carcinoma.Genome medicine · 2024Article
- Accurate estimation of molecular counts from amplicon sequence data with unique molecular identifiers.Bioinformatics (Oxford, England) · 2023Article
- Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing.Genome research · 2022Article
- A replication-linked mutational gradient drives somatic mutation accumulation and influences germline polymorphisms and genome composition in mitochondrial DNA.Nucleic acids research · 2021Article
- Increased yields of duplex sequencing data by a series of quality control tools.NAR genomics and bioinformatics · 2021Article
- STAMP: a multiplex sequencing method for simultaneous evaluation of mitochondrial DNA heteroplasmies and content.NAR genomics and bioinformatics · 2020Article
- Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues.PLoS biology · 2020Article
- Family reunion via error correction: an efficient analysis of duplex sequencing data.BMC bioinformatics · 2020Article
- SinoDuplex: An Improved Duplex Sequencing Approach to Detect Low-frequency Variants in Plasma cfDNA Samples.Genomics, proteomics & bioinformatics · 2020Article
- Development and Application of Duplex Sequencing Strategy for Cell-Free DNA-Based Longitudinal Monitoring of Stage IV Colorectal Cancer.The Journal of molecular diagnostics : JMD · 2019Article
- A High-Resolution View of Adaptive Event Dynamics in a Plasmid.Genome biology and evolution · 2019Article
- Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations.Nature reviews. Genetics · 2018Review
- Recent Advances in Detecting Mitochondrial DNA Heteroplasmic Variations.Molecules (Basel, Switzerland) · 2018Review
- Targeted error-suppressed quantification of circulating tumor DNA using semi-degenerate barcoded adapters and biotinylated baits.Scientific reports · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Duplex sequencing was originally developed to detect rare nucleotide polymorphisms normally obscured by the noise of high-throughput sequencing. Here we describe a new, streamlined, reference-free approach for the analysis of duplex sequencing data. We show the approach performs well on simulated data and precisely reproduces previously published results and apply it to a newly produced dataset, enabling us to type low-frequency variants in human mitochondrial DNA. Finally, we provide all necessary tools as stand-alone components as well as integrate them into the Galaxy platform. All analyses performed in this manuscript can be repeated exactly as described at http://usegalaxy.org/duplex .
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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.