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

all my dirty r-scripts

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.

A pipeline to analyse marine fish amplicon data

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

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

Amplicon sequencing workflow with snakemake and dada2 (MiSeq data)

Bioinformatic data analysis scripts for RNA-seq and metagenomic sequencing data

DADA2 pipeline for nitrogenase (nifH) amplicon sequences (Illumina paired-end)

A workflow for processing CCS reads of AMF to ASVs using DADA2

National workshop on microbiome informatics

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

En este repositorio se encuentran todos los scripts utilizados para mi tesis de licenciatura, titulada: "Análisis de perfiles funcionales de la microbiota intestinal de pacientes con trastorno depresivo mayor", la cual utiliza un lenguaje de programación en R y Phyton.

Generalized dada2 workflow. Refer to the wiki for help and troubleshooting.

Code and repository links for Klein & Frühe et al. 2024

A repository containing a demo microbiome workflow for R and Python

neonMicrobe: Processing NEON soil microbe marker gene sequence data into ASV tables, duplicated from https://github.com/claraqin/neonMicrobe

Analysis of Salmo trutta gametes and embryo microbiome project in Vals/Trun, Switzerland

The purpose of this repository is to store R scripts that were used for 16S community compositional analyses.

Microbiome analysis pipeline with reference tutorial. This code was written in October 2024 to process rRNA marker gene data (16S and ITS) from rhizosphere soil samples.

Here we discuss strategies and workflows to analyse metagenomics datasets