A repository containing a demo microbiome workflow for R and Python

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

This repositorey contain the dada2 pipeline used to process the illumina sequence reads in the manuscript "Temporal variability in the growth-enhancing effects of different bacteria within the microbiome of the diatom Actinocyclus sp." (DOI: 10.3389/fmicb.2023.1230349)

National workshop on microbiome informatics

CUSO Microbiome analysis workshop 2020

This is repository of amplicon sequencing data and bioinformatics pipeline codes for the nectar microbiome of Monkey Flowers.

Here we discuss strategies and workflows to analyse metagenomics datasets

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

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

Metabarcoding analysis pipeline, using DADA2 and qiime2

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

Accurate sample inference from amplicon data with single nucleotide resolution

Processing of 16S rRNA gene amplicon sequences from from Samail Ophiolite, Oman

Reconstructing a dada2 pipeline with batch processing using an OOP design

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

Modified dada2 script, used for master's thesis project. Takes fast2 files and outputs ASV table, taxonomy table, phylogenetic tree, and input files for PICRUSt2

Introduction to 16S Amplicon Sequencing Data Analysis using DADA2

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

Bioinformatic data analysis scripts and pipelines