Welcome to your origin story as a bioinformatician!
This training will guide you from:
“What is this terminal thing?”
to
“Ah yes, this phylogenetic tree tells a story.”
This repository will contain:
- hands-on exercises
- real-world datasets
- step-by-step workflows
- genomic epidemiology interpretation
| Module | Topic | Skills |
|---|---|---|
| 01 | Linux Command Line | file navigation, text processing |
| 02 | NGS Data QC | nanopore QC, trimming |
| 03 | Bioinformatics Workflows | metagenomics, alignment, consensus |
| 04 | Downstream Analysis | phylogenetics, clade interpretation |
Pathogen genomics helps us:
- track outbreaks
- understand transmission
- detect emerging variants
- support public health decisions
“We are basically detectives… but for genomes.”
The training materials will be organized as follows:
pathogen-genomics-training/
│
├── module-01-linux/
├── module-02-ngs-qc/
├── module-03-workflows/
└── module-04-downstream-analysis/
Each module will contain:
- step-by-step guides
- exercises
- datasets (or download links)
- expected outputs
🚧 This repository is currently under development. Stay tuned 👀!
Good news: you will be provided with a training virtual machine (VM) where you will do all the analyses.
Bad news: the command line still requires typing. 😂
Participants only need tools to connect, analyze, and download results.
Used to connect to the training VM.
Participants must have access to one of the following:
| Operating System | Recommended Tool |
|---|---|
| 🐧 Linux | Terminal |
| 🍎 Mac | Terminal |
| 🪟 Windows | WSL, Command Prompt or PowerShell |
Used for:
- Nextclade/Nextstrain
- Pavian visualization
- Database access
- occasional panic-Googling
- ask AI for help 🤭
Recommended browsers:
- Google Chrome
- Brave
- Firefox
Used to download results from the VM to your laptop.
| Operating System | Recommended Tool |
|---|---|
| 🪟 Windows | WinSCP |
| 🍎 Mac | Cyberduck or FileZilla |
| 🐧 Linux | FileZilla |
Participants should have:
- laptop 💻 (any laptop capable of running the tools listed below; no special specifications required)
- terminal or SSH client 🔐
- web browser 🌐
- file transfer software 📂
- curiosity 🧠
- patience 🥲
This training is designed for participants with basic knowledge of bioinformatics but limited practical experience
No prior coding experience is required.
Participants should be familiar with:
- DNA and genes
- basic concept of pathogens
- general idea of sequencing
If you know that:
DNA ≠ WiFi password
you are ready.
Participants should be comfortable with:
- using a computer
- copying and pasting commands
- navigating folders
- downloading files
- not renaming files to
final_final_v3_reallyfinal.fastq
- prior exposure to FASTA or FASTQ files
- familiarity with genomics
- basic command line experience
- emotional attachment to Linux terminals
We will guide you through everything step-by-step.
- accept that typos happen
- accept that errors happen
- accept that debugging is part of the journey
- accept that the pipeline sometimes works only when observed
Must be a memer.
Example acceptable responses to errors:
"Have you tried turning it off and on again?"
"It worked yesterday."
"Who wrote this script?"
"Oh... I forgot to activate the environment."
"Why is there a space in the filename?"
"Permission denied... but I feel permitted."
- every folder contains another folder
- every tool requires another dependency
- every dataset has one weird sample
- every command works after the third try
- every pipeline produces at least one plot nobody understands at first
- copy-paste is encouraged
- reading error messages is a life skill
- Google is part of the workflow
- breaks improve reproducibility
- hydration improves debugging accuracy
"In theory, theory and practice are the same.
In practice, they are not." – every bioinformatician ever
You are ready 🚀
For those who want to go deeper (or accidentally became the “bioinformatics person” in the lab 👀)
"Half of bioinformatics is knowing what to Google.
The other half is knowing which result is correct."
- https://linuxcommand.org/lc3_learning_the_shell.php
- https://explainshell.com/ (type a command → see what each part does 🔥)
- https://docs.conda.io/en/latest/
- https://docs.nextstrain.org/
If you're feeling curious (or brave):
- bash scripting (
forloops, variables) - environment management
- workflow automation
-
Realingo AML, Polotan FGM, Abulencia MFP, et al. Integration of bioinformatic tools for the detection of SARS-CoV-2 co-infection cases. Microbial Genomics 2026;12(1):mgen001604. https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001604
-
Lu J, Rincon N, Wood DE, Breitwieser FP, et al. Metagenome analysis using the Kraken software suite. Nat Protoc. 2022;17:2815–2839. https://pmc.ncbi.nlm.nih.gov/articles/PMC9725748/
-
Aksamentov I, Roemer C, Hodcroft EB, Neher RA. Nextclade: clade assignment, mutation calling and quality control for viral genomes. Journal of Open Source Software. 2021;6(67):3773. https://joss.theoj.org/papers/10.21105/joss.03773
-
Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018;34(23):4121-4123. https://academic.oup.com/bioinformatics/article/34/23/4121/5001388
-
ARTIC Network field bioinformatics pipeline - https://github.com/artic-network/fieldbioinformatics
-
Kraken2 - https://github.com/DerrickWood/kraken2
-
Minimap2 - https://github.com/lh3/minimap2
-
Samtools - https://github.com/samtools/samtools
Reading these may cause:
- sudden understanding of error messages
- improved debugging skills
- people asking you for help
- you saying “it depends” more often
"The best bioinformaticians are not the ones who memorize commands,
but the ones who know how to figure things out."
You're officially beyond the slides 🚀
If you want to perform bioinformatics analysis on your own local computer using miniconda:
| 🪟 Windows | Install WSL-Ubuntu | Install miniconda -- follow linux installation |
| 🍎 Mac | Use your terminal |
