## Who this is for
You work at the bench. Someone has sent you a folder of sequencing reads, or told you the analysis “just runs on the cluster”, and every set of instructions you find assumes you already know what a terminal is.
This course assumes you don’t. It starts at the point where you open a black window and have no idea what to type.
## Why bother
Two things change once the terminal stops being frightening.
You stop doing things by hand. Renaming two hundred files, counting lines across fifty CSVs, pulling every sequence matching a pattern — these go from an afternoon to one line.
You can use the tools. Most bioinformatics software has no buttons. Assembly, annotation, alignment and quality control are command-line programs, and no amount of clicking will reach them.
## What you’ll actually be doing
You will type commands and watch what happens. Every module is hands-on, and every example uses the same practice dataset — a small set of phage files you’ll download in Module 0: a FASTA, plate counts from a dilution series, and a log file from a real assembly run.
Nothing is abstract. When you learn pipes, you use them to find which host strain appears most often in your plate data. When you write your first script, it counts the reads in every FASTA in a folder. The capstone puts the whole course together into one small working pipeline, with the expected output given so you can check yourself.
## You will not break anything
Everything happens inside one practice folder you create at the start, and you will never be asked to type `sudo`.
Two commands can genuinely lose work: `rm`, which deletes permanently with no recycle bin, and `>`, which overwrites a file without warning. Both get a careful treatment at the point they appear, along with the habits that stop them biting. Everything else is safe to get wrong — and getting it wrong is how this is learned.
## How the course works
Ten steps, in order. Each one unlocks when you mark the previous one complete, so nothing gets skipped by accident.
Work at your own pace. Your progress is saved, and you can stop and return whenever you want. Finish every step and a verifiable certificate is issued to your dashboard.
Module 0 is setup and sits outside the timings: installing a working terminal and downloading the practice data, about 45 minutes. Do it on the machine you’ll be using throughout, before you start Module 1.
## What this course does not cover
This is the foundation, not the destination. It does not teach Python, R, git, or any specific bioinformatics tool, and it does not cover connecting to a remote server or running jobs on a cluster.
What it does is make all of those learnable. Every one of them assumes the command line, and this is where you get it.