When I started my journey into microbiome research, I was completely new to the field.I had no clue what I was doing. Zilch. Nada. But I was determined to learn—not just the science, but also the bioinformatics involved. So, like any eager newbie, I followed every tutorial I could find. And guess what? They worked beautifully…on their sample data. Then came the moment of truth: using my own data. That’s when the real struggle began. Steps that seemed crystal clear with example datasets turned into a tangled mess with my files. Suddenly, “easy” tutorials became confusing, frustrating, and downright maddening. To be fair, I don’t blame the authors of those tutorials. Maybe—just maybe—they wrote them assuming their readers already had some background in bioinformatics and coding. Perhaps they never imagined a total newbie like me would be bold (or crazy) enough to give them a try!

This guide is the product of my trials, errors, and eventual triumphs. This guide is all about harnessing the power of R for 16S rRNA data analysis using a mix of awesome packages like microeco, metacoder, and microbiotaprocess (among others). The pipeline I’ve laid out is cobbled together from half a dozen online tutorials, each offering a nugget of wisdom but often leaving big gaps to fill. I’ve taken those pieces, filled in the blanks, and turned it into a cohesive roadmap that works—especially when you’re using your own data!

Disclaimer;

Here’s the deal: this pipeline is for research purposes only. It’s not a magic wand, and I can’t promise perfect results. You’re still responsible for checking your data quality and interpreting your results based on your research goals. This guide is offered “as is,” and I can’t be held liable for errors or unexpected outcomes. If your research is critical, double-check everything and consult an expert if needed.

Why I Wrote This Guide;

Let’s be real: no one should have to waste hours figuring out how to prep and format data for analysis. That’s why I wrote this guide—to save you time and sanity. If you’re planning to use the microeco pipeline, this will walk you through the setup process step by step, so you can get straight to the fun part: analyzing your microbiome data.

Enough about the struggles—let’s move forward and dive into the solutions. It’s time to get our raw sequences ready and set the stage for some serious analysis.