ArticleBMC genomics2016
A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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
23 citing papers in PubMed, 44 citations in OpenAlex.
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- Enhancing Clinical Applications by Evaluation of Sensitivity and Specificity in Whole Exome Sequencing.International journal of molecular sciences · 2024Article
- From Genomic Exploration to Personalized Treatment: Next-Generation Sequencing in Oncology.Current issues in molecular biology · 2024Review
- Mutational fitness landscape of human influenza H3N2 neuraminidase.Cell reports · 2023Article
- CRISPR/Cas9 and next generation sequencing in the personalized treatment of Cancer.Molecular cancer · 2022Review
- The Liquid Biopsy for Lung Cancer: State of the Art, Limitations and Future Developments.Cancers · 2021Review
- DiMSum: an error model and pipeline for analyzing deep mutational scanning data and diagnosing common experimental pathologies.Genome biology · 2020Article
- Benchmarking of computational error-correction methods for next-generation sequencing data.Genome biology · 2020Article
- Teaching an Old Virus New Tricks: A Review on New Approaches to Study Age-Old Questions in Influenza Biology.Journal of molecular biology · 2019Review
- Rational "Error Elimination" Approach to Evaluating Molecular Barcoded Next-Generation Sequencing Data Identifies Low-Frequency Mutations in Hematologic Malignancies.The Journal of molecular diagnostics : JMD · 2019Article
- A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project.Frontiers in genetics · 2019Review
- HCV transmission in high-risk communities in Bulgaria.PloS one · 2019Article
- Article
- Multiplexed assays of variant effects contribute to a growing genotype-phenotype atlas.Human genetics · 2018Review
- Systematic evaluation of error rates and causes in short samples in next-generation sequencing.Scientific reports · 2018Article
- Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations.Nature reviews. Genetics · 2018Review
- A framework for exhaustively mapping functional missense variants.Molecular systems biology · 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
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundThe high error rate of next generation sequencing (NGS) restricts some of its applications, such as monitoring virus mutations and detecting rare mutations in tumors. There are two commonly employed sequencing library preparation strategies to improve sequencing accuracy by correcting sequencing errors: read-pairing method and tag-clustering method (i.e. primer ID or UID). Here, we constructed a homogeneous library from a single clone, and compared the variant calling accuracy of these error-correction methods.
resultWe comprehensively described the strengths and pitfalls of these methods. We found that both read-pairing and tag-clustering methods significantly decreased sequencing error rate. While the read-pairing method was more effective than the tag-clustering method at correcting insertion and deletion errors, it was not as effective as the tag-clustering method at correcting substitution errors. In addition, we observed that when the read quality was poor, the tag-clustering method led to huge coverage loss. We also tested the effect of applying quality score filtering to the error-correction methods and demonstrated that quality score filtering was able to impose a minor, yet statistically significant improvement to the error-correction methods tested in this study.
conclusionOur study provides a benchmark for researchers to select suitable error-correction methods based on the goal of the experiment by balancing the trade-off between sequencing cost (i.e. sequencing coverage requirement) and detection sensitivity.
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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.