dada2

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

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

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

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

A pipeline to analyse marine fish amplicon data

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)

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

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.

National workshop on microbiome informatics

Accurate sample inference from amplicon data with single nucleotide resolution

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

R package for post-denoising ASV refinement in metabarcoding workflows, using CLEAN/DIRTY ASV reconciliation to reduce artifact ASVs and Phred-score-related bias.

Micro-substitution chimera / PCR artifact detection for PacBio full-length 16S rRNA amplicon sequencing; to be run on sequence tables after DADA2 or other denoisers.

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

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