The practice terminal further down is great for learning the commands, but eventually you’ll want a real one open on your own computer. Pick your operating system below.

When you open a terminal, you’ll see something like this, called a prompt. It’s waiting for you to type a command and press Enter.

trainee@yourcomputer:~$ _

Everything you do lives inside folders (called directories in bash-speak), just like Finder or File Explorer — except you navigate them by typing, not clicking.

Three commands answer almost every “where am I” question:

# Print Working Directory — shows exactly where you are
pwd

# LiSt — shows what's inside the current folder
ls

# Change Directory — move into a folder
cd reads

Once you can move around, you’ll want to create, copy, and clean up:

# MaKe DIRectory — create a new folder
mkdir results

# create an empty file
touch notes.txt

# CoPy a file
cp genome.fasta results/genome_backup.fasta

# MoVe (or rename) a file
mv notes.txt results/notes.txt

# ReMove — careful, this doesn't go to a Recycle Bin!
rm old_file.txt

cat prints a file’s contents straight to the screen — great for a quick peek at something small:

cat notes.txt

echo prints text back at you — and combined with >, it can write that text into a file:

# prints to the screen
echo "Phages are viruses that infect bacteria"

# the > sends the output into a file instead of the screen
echo "Phages are viruses that infect bacteria" > notes.txt

A few habits that make the terminal dramatically faster and friendlier:

# press Tab while typing a name — it auto-completes it for you
cd rea[Tab]

# * is a wildcard — matches anything
ls *.fastq

# | (pipe) sends one command's output into another
cat notes.txt | grep phage

# almost every tool will explain itself if you ask
ls --help

This is a real, working (simulated) terminal — type into it below. You start in a home folder with a few sample phage files already inside. Type help to see everything it understands.