Research Articles
Mastering DADA2's min_overlap Parameter: A Practical Guide for Biomedical Researchers
This comprehensive guide explores the critical role of DADA2's `min_overlap` parameter in 16S rRNA amplicon sequencing analysis.
DADA2 maxEE Explained: A Complete Guide to Error Threshold Filtering for Microbiome Researchers
This comprehensive guide demystifies the critical maxEE parameter within the DADA2 pipeline, used for high-throughput amplicon sequence analysis.
DADA2 Error Correction for Illumina Data: A Complete Guide for Accurate Amplicon Sequence Variant Analysis
This comprehensive guide provides researchers, scientists, and drug development professionals with a complete workflow for implementing the DADA2 pipeline to correct sequencing errors in Illumina amplicon data.
Demystifying DADA2: A Comprehensive Guide to Troubleshooting 'Plugin Error' in R for Robust Microbiome Analysis
This article provides a definitive guide for researchers, scientists, and bioinformaticians encountering the DADA2 'plugin error' in R.
DADA2 Processing for Large Datasets: Complete Optimization Guide for Faster Amplicon Analysis
This comprehensive guide addresses the critical challenge of processing large 16S rRNA amplicon sequencing datasets with DADA2 efficiently.
DADA2 ASVs in Microbial Research: A Comprehensive Guide from Theory to Application for Scientists
This article provides a complete resource on DADA2 (Divisive Amplicon Denoising Algorithm) for generating high-resolution Amplicon Sequence Variants (ASVs).
DADA2 vs QIIME2 vs MOTHUR: A 2025 Reproducibility Benchmark for Clinical Microbiome Analysis
This comprehensive review critically compares the DADA2, QIIME2, and MOTHUR pipelines for 16S rRNA amplicon sequence data analysis, with a focus on reproducibility in biomedical research.
Resolving the DADA2 derep() Error: Understanding and Fixing the NA/Integer Overflow Issue in Microbiome Analysis
This article addresses a critical computational error in the DADA2 pipeline where the derep() function fails, returning NA values due to an integer overflow when processing exceptionally large or deep...
DADA2 vs Deblur vs QIIME2: A 2024 Comparative Guide for Microbiome Denoising in Biomedical Research
This comprehensive guide compares the three leading denoising algorithms—DADA2, Deblur, and QIIME2's core features—for 16S rRNA amplicon sequence analysis.
ZINB vs. Hurdle Models: A Practical Guide for Biomedical Research and Drug Development
This article provides researchers, scientists, and drug development professionals with a comprehensive comparison of Zero-Inflated Negative Binomial (ZINB) and hurdle models for analyzing over-dispersed count data with excess zeros.