Lesson 1 — What Is a Bash Script and Why Use One?

Learning Objectives

By the end of this lesson, you will be able to:

• Describe the problem that Bash scripts solve
• Explain what a Bash script is in plain language
• Recognise what a simple script looks like before writing one

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1. The Problem of Repetition

Imagine you have just received sequencing data for a project: 20 FASTQ files, one for each sample. Your first task is quality control — running FastQC on every file.

So you open the terminal and start typing:

fastqc Training/short_reads/paired/SRR1553607_1.fastq

Then the second file:

fastqc Training/short_reads/paired/SRR1553607_2.fastq

And so on, 18 more times.

This approach has several problems:

• It is slow. Typing 20 commands takes time, even with copy-paste.
• It is error-prone. One mistyped filename and you have run quality control on the wrong file — or no file at all.
• It is not reproducible. Six months later, your collaborator asks exactly which files you ran. You will not remember.
• It does not scale. What happens when the next project has 200 samples?

There is a better way.

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2. What Is a Bash Script?

A Bash script is a plain text file that contains a list of commands. When you run the script, Bash reads the file from top to bottom and executes each command in order — exactly as if you had typed them yourself.

That is the whole idea. There is no magic here. A script is just a saved list of commands.

Here is what a simple script looks like:

#!/bin/bash

echo "Starting quality control..."
fastqc Training/short_reads/paired/SRR1553607_1.fastq
fastqc Training/short_reads/paired/SRR1553607_2.fastq
echo "Done."

You will learn exactly what each part of this script means in the lessons that follow. For now, notice that it looks almost identical to the commands you already know — because it is.

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3. Why Scripts Matter in Bioinformatics

Bash scripts are not just a convenience. In bioinformatics, they serve several important purposes:

Reproducibility. A script is a record of exactly what you ran, in what order, on which files. This matters when you need to re-run an analysis, when a reviewer asks for your methods, or when a collaborator needs to repeat your work.

Automation. Once a script works on two files, making it work on two hundred is a small change. You will see how in Lesson 4.

Fewer mistakes. Typing the same command 20 times introduces 20 opportunities for a typo. Running a script introduces one.

A foundation for more. Every bioinformatics pipeline — from simple QC checks to whole-genome assembly workflows — is built on scripts. Learning to write them opens up the entire field.

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4. What You Will Build in This Module

By Lesson 5, you will have written a script that:

1. Stores a folder path in a variable
2. Loops over every FASTQ file in that folder
3. Extracts a clean sample name from each filename
4. Runs FastQC on each file
5. Prints a message confirming each file was processed

It will look like this:

#!/bin/bash

DATA_DIR="Training/short_reads/paired"

for FILE in $DATA_DIR/*.fastq
do
    SAMPLE=$(basename $FILE .fastq)
    echo "Processing: $SAMPLE"
    fastqc $FILE
done

echo "All samples processed."

If any part of this looks unfamiliar right now, that is expected. Each concept — variables, basename, loops — gets its own lesson. By the time you reach Lesson 5, every line will make sense.

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Summary

• A Bash script is a text file containing commands that Bash executes in order
• Scripts solve the problem of repetition: run many files with one command
• In bioinformatics, scripts improve reproducibility, reduce errors, and enable automation
• This module builds toward a complete script step by step

In the next lesson, you will write your very first script and learn the most important line it must contain.