A practical beginner series · Free to follow
Bioinformatics on a Windows PC.
From FASTQ to Phylogeny
For wet-lab scientists, students, and anyone taking their first steps at the command line. Start with the computer you already use, and build your understanding one small exercise at a time.
The learning path
Begin with the basics.
Four lessons take you from setting up your workspace to understanding sequence files, quality scores, and your first FastQC reports.
- Series introduction
From the laboratory bench to the command line
Why I started this series, who it is for, and what I hope to make easier.
Read the announcement on LinkedIn ↗ - Available now · Beginner
Set up WSL2 and Ubuntu
Open a Linux environment on Windows, try your first commands, and create a tidy workspace for the exercises ahead.
About 10 minutes of hands-on practice, plus installation and restart time.
- Available now · Beginner
FASTA vs FASTQ
Connect the wet lab to FASTQ, learn where FASTA comes from, then create and inspect two tiny practice files.
Eight slides and a 10-minute challenge. No new software to install.
- Available now · Beginner
Can I trust this base? Understanding FASTQ quality scores
Connect sequencing signals to confidence, interpret Phred scores, and decode a mixed-quality read one base at a time.
Eight slides and a 10-minute challenge. No new software to install.
- Latest lesson · Available now
One read is easy. What about millions? Assessing sequencing data with FastQC
Install FastQC in Ubuntu, compare two practice datasets, and learn what the quality plots and report flags can tell you.
Eight slides, two downloadable FASTQ datasets, and a 10-minute challenge.
- Coming next
Which FastQC warnings matter, and what should you do next?
Connect the patterns in your report to decisions about the next step.
The next exercise in the series.
Why this series
I started at the bench, too.
I came into bioinformatics from a wet-lab background. Learning to connect the data I generated with the work needed to understand it shaped how I now teach.
In this series, I explain what we are doing, why it matters, and how each step connects to the next. The exercises begin with a working environment and basic files before moving into analysis.
Explore my teaching and training work →Learn together
Try the exercise. Bring your questions.
The LinkedIn lesson posts are the place to discuss each exercise and share where you got stuck. This page keeps the series in order so you can return to the right step.