Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

This pipeline is intended to be a convenient way to work though large sets of metagenomic or metatranscriptiomic datasets while also retaining high analytical flexibility due to retained intermediate results that might be useful outside of the intended purpose.

This repository provides scripts for the 16S microbiome analysis and metagenome prediction using linux and R-Studio

microbiome analysis of ant colonies

Docker RStudio container for Duke University IBIEM 2017 - Integrative Bioinformatics for Investigating & Engineering Microbiomes

Codes for the statistical analysis that investigates the impact of high-fat diet on gut microbiome and serotonergic gene expression in the raphe nuclei.

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.

Extract and compare variable regions from hCom genomes.

Bash scripts for running QIIME 1.9 and a Snakemake workflow to automate it using singularity container images.

Code for 4th year honours thesis project at the University of Waterloo.

16S Microbiome Analysis Pipeline. This version written in Nextflow.

microbiome analysis of ant colonies