Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

Amplicon sequence processing workflow using QIIME 2 and Snakemake

16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/

Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.

Dadaist2 🟨 Highway to R

Processing NEON soil microbe marker gene sequence data into ASV tables.

Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project

Working Demo on 16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Visit repo website for HTML output

A repository with a general dada2 pipeline for amplicon processing

A metabarcoding pipeline for analysing Illumina amplicon data.

Qiime2 and DADA2 are one of the latest bioinformatics tools used in 16S RNA analysis. The current Qiime2 and DADA2 pipelines support End to End 16S RNA analysis, among other analyses.

all my dirty r-scripts

A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.

Unified short-read workflow for multi-marker amplicon (16S, ITS, 18S, gyrB, rpoB) and shotgun taxonomic profiling. Snakemake, conda-based, reproducible.

Python-first amplicon denoising — byte-identical to R's DADA2

A pipeline to analyse marine fish amplicon data

End-to-end 16S microbiome analysis (FASTQ to PCoA) of Crohn's Disease. Implements a QIIME 2 & Docker pipeline to identify significant phylogenetic dysbiosis (p=0.0007).

Workflow stages and data for Morando, Magasin et al. 2025

🌊 16S rRNA microbiome data analysis workflow using DADA2 and R on a high performance cluster using SLURM

Amplicon sequencing workflow with snakemake and dada2 (MiSeq data)