ArticlemSystems2023
Effects of error, chimera, bias, and GC content on the accuracy of amplicon sequencing.
Article in mSystems, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- Accounting for Variability Across Years, Depths, and Non-Target Reads Improves Quantification of Root Community Composition in Plant Mixtures.Molecular ecology resources · 2026Article
- Experimental evidence for early bacterial inheritance in the giant kelp, Macrocystis pyrifera.FEMS microbiology ecology · 2026Article
- Dual-SVF: a robust knowledge-guided multimodal method for structural variant filtering in long-read sequencing.Briefings in bioinformatics · 2026Article
- NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.BMC bioinformatics · 2026Article
- AmpliFuse: an amplicon simulation tool with enhanced chimera generation for Illumina platforms.Microbiology resource announcements · 2026Article
- A novel targeted hybrid capture-NGS assay for sensitive detection of multiplex respiratory pathogens.Microbiology spectrum · 2026Article
- Revised 16S rRNA V4 hypervariable region targeting primers enhance detection of Patescibacteria and other lineages across diverse environments.ISME communications · 2026Article
- Optimized MT-Capture targeted enrichment sequencing for the complete genome of norovirus in stool and sewage samples.Frontiers in microbiology · 2026Article
- Article
- Long-range PCR and Nanopore sequencing for localisation and phasing variants: an end-to-end clinical application workflow.BMC medical genomics · 2025Article
- Comparison of QIIME1 and QIIME2 for Analyzing Fungal Samples from Various Built Environments.Microorganisms · 2025Article
- Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research?Poultry science · 2025Review
- Patterns and drivers of diatom diversity and abundance in the global ocean.Nature communications · 2025Article
- Targeted 16S rRNA Gene Sequencing for Water Samples.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data.Briefings in bioinformatics · 2024Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
importanceAmplicon sequencing of targeted genes is the predominant approach to estimate the membership and structure of microbial communities. However, accurate reconstruction of community composition is difficult due to sequencing errors, and other methodological biases and effective approaches to overcome these challenges are essential. Using a mock community of 33 phylogenetically diverse strains, this study evaluated the effect of GC content on sequencing results and tested different approaches to improve overall sequencing accuracy while characterizing the pros and cons of popular amplicon sequence data processing approaches. The sequencing results from this study can serve as a benchmarking data set for future algorithmic improvements. Furthermore, the new insights on sequencing error, chimera formation, and GC bias from this study will help enhance the quality of amplicon sequencing studies and support the development of new data analysis approaches.
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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.