Tutorials & Workshops

Curated learning resources for bioinformatics

Overview

This page contains a comprehensive, searchable catalogue of tutorials, courses, and workshops for bioinformatics. Resources are organized by topic and source, with most being free and self-paced.

How to Use This Catalogue

Use browser search (Ctrl/Cmd+F) to find specific topics
Start with foundational skills (Linux, programming) before diving into advanced genomics
Many courses can be audited for free - look for “Free/self-paced” access
Track your progress using the Analysis Catalogue Template

Genomics & NGS

Short-Read Sequencing

Genome bioinformatics: from short- to long-read sequencing

Provider: EMBL-EBI
Topics: NGS & long-read sequencing, variant calling, workflows
Access: Free / self-paced
Link: Course Page

What you’ll learn: Comprehensive introduction to genome sequencing technologies, transitioning from short-read to long-read approaches, with practical variant calling examples.

Genome bioinformatics: resequencing & variant calling

Provider: EMBL-EBI
Topics: Short-read variant calling, quality control
Access: Free / self-paced
Link: Course Materials

What you’ll learn: Hands-on variant calling workflow from raw sequencing data through to filtered, annotated variants.

Data Wrangling and Processing for Genomics

Provider: The Carpentries
Topics: FASTQ, QC, mapping, variant calling preparation
Access: Free / self-paced
Link: Course Page

What you’ll learn: Essential skills for processing genomic data including quality control, trimming, alignment, and preparing data for variant calling.

Introduction to Next-Generation Sequencing Technologies

Provider: OmicsTutorials
Topics: NGS background
Access: Video tutorial
Link: Watch Video

Structural Variants

Structural Variant detection and comparison (SVs)

Provider: Physalia Courses
Topics: SV detection, SV comparison
Access: Some materials open
Link: Course Page

What you’ll learn: Methods for detecting and analyzing structural variations including deletions, duplications, inversions, and translocations.

Variant Annotation & Analysis

Exploring genotype–phenotype data using Ensembl

Provider: EMBL-EBI
Topics: Variant annotation, phenotype links
Access: Self-paced
Link: Course Page

Variant calling and annotation (FutureLearn)

Provider: FutureLearn
Topics: SNV/indel calling, annotation
Access: Free (register to audit)
Link: Course Page

Population & Complex Trait Genetics

GWAS & Polygenic Scores

GWAS Catalog

Provider: EMBL-EBI
Topics: GWAS data exploration, variant annotation
Access: Free / self-paced
Link: Course Page

What you’ll learn: How to navigate and interpret GWAS results, understand genome-wide significance, and explore disease-associated variants.

Calculating polygenic scores with the Polygenic Score Catalog Calculator

Provider: EMBL-EBI
Topics: PRS / PGS Catalog usage
Access: Webinar (on-demand)
Link: Webinar

What you’ll learn: How to calculate and interpret polygenic risk scores for complex traits and diseases.

Analysing linkage disequilibrium with Ensembl

Provider: EMBL-EBI
Topics: LD analysis, population genetics
Access: Webinar (on-demand)
Link: Webinar

Translational Genomics

From variant to drug target: using the expanded toolbox

Provider: EMBL-EBI
Topics: Translational genomics, target prioritisation
Access: Free / self-paced
Link: Course Page

What you’ll learn: How to move from genetic variants identified in GWAS to potential therapeutic targets.

Functional Genomics

Functional Genomics I–III

Provider: EMBL-EBI
Topics: Experimental design, gene regulation, functional assays
Access: Free / self-paced
Link: Course Series

What you’ll learn: Comprehensive introduction to functional genomics including ChIP-seq, ATAC-seq, and other regulatory genomics approaches.

Functional Genomics: From Data to Biological Insight

Provider: OmicsTutorials
Topics: Functional genomics overview & tools
Access: Article / guide
Link: Read Article

Multi-Omics & Integration

Introduction to multi-omics data integration and visualisation

Provider: EMBL-EBI
Topics: Multi-omics integration, visualization
Access: Self-paced
Link: Course Materials

What you’ll learn: Methods for integrating genomics, transcriptomics, proteomics, and other omics data types for comprehensive biological insights.

Dementia-Specific Resources

Data-driven approaches to understanding dementia

Provider: EMBL-EBI
Topics: Systems / omics approaches to dementia
Access: Webinar (on-demand)
Link: Webinar

What you’ll learn: How genomics, transcriptomics, and other data-driven approaches are being applied to understand dementia mechanisms and identify therapeutic targets.

Workflow Management

Snakemake

Snakemake for Bioinformatics

Provider: Carpentries Incubator
Topics: Snakemake basics, rules, conda, workflows
Access: Free / self-paced
Link: Course Page

What you’ll learn: Build reproducible, scalable bioinformatics pipelines using Snakemake.

Galaxy Training: Snakemake Tutorial

Provider: Galaxy Project
Topics: Workflow automation, Make → Snakemake transition
Access: Free / self-paced
Link: Tutorial

Reproducible and Scalable Research with Snakemake & Containers

Provider: SIB Swiss Institute of Bioinformatics
Topics: Snakemake, Docker/Singularity, reproducibility
Access: Free materials
Link: Training Materials

Nextflow

Deploying Nextflow pipelines in the cloud

Provider: EMBL-EBI
Topics: Nextflow, workflow management
Access: Webinar (on-demand)
Link: Webinar

Introduction to Workflow Tool Nextflow

Provider: ARCCA
Topics: Workflow management with Nextflow
Access: Recorded sessions / material
Link: ARCCA Training

Reproducibility

Reproducibility in Bioinformatics

Provider: Physalia Courses
Topics: Containers, versioning, Snakemake
Access: Some slides/materials open
Link: Course Page

Programming Languages

Python

Programming with Python

Provider: Software Carpentry
Topics: Python basics
Access: Free / self-paced
Link: Course Page

What you’ll learn: Python fundamentals including variables, loops, functions, and data structures - essential for bioinformatics scripting.

Plotting and Programming in Python

Provider: Data Carpentry
Topics: Python + matplotlib
Access: Free / self-paced
Link: Course Page

What you’ll learn: Python programming with a focus on data analysis and visualization using matplotlib and pandas.

Introduction to Python

Provider: ARCCA
Topics: Python basics, HPC adaptation
Access: Recorded sessions
Link: ARCCA Training

Advanced Python

Provider: ARCCA
Topics: Advanced Python programming
Access: Recorded sessions
Link: ARCCA Training

R Programming

Programming with R

Provider: Software Carpentry
Topics: R basics
Access: Free / self-paced
Link: Course Page

What you’ll learn: R fundamentals for data analysis and statistical computing.

R for Reproducible Scientific Analysis

Provider: Software Carpentry
Topics: R workflows, reproducibility
Access: Free / self-paced
Link: Course Page

Databases & SQL

Databases and SQL

Provider: Software Carpentry
Topics: SQL basics, relational queries
Access: Free / self-paced
Link: Course Page

What you’ll learn: Query databases using SQL - useful for working with genomic databases and large datasets.

Version Control

Version Control with Git

Provider: Software Carpentry
Topics: Git, commits, branches, GitHub
Access: Free / self-paced
Link: Course Page

What you’ll learn: Essential Git skills for version controlling code and collaborating on projects. Critical skill for reproducible research.

Linux & Command Line

Introduction to Linux with Command Line

Provider: ARCCA
Topics: Linux CLI basics, navigation, commands
Access: Recorded sessions + material
Link: ARCCA Training

What you’ll learn: Navigate and use the Linux command line - absolutely essential for bioinformatics work.

Introduction to Linux Shell Scripting

Provider: ARCCA
Topics: Writing shell scripts, loops, automation
Access: Recorded sessions + material
Link: ARCCA Training

Comprehensive Guide to Setting up and Using Linux for Bioinformatics Analysis

Provider: OmicsTutorials
Topics: Linux setup, shell basics, tooling for bioinformatics
Access: Article / guide
Link: Read Guide

Mastering Bioinformatics Analysis with FASTA Sequences

Provider: OmicsTutorials
Topics: FASTA workflows, Unix/Linux skills
Access: Article / guide
Link: Read Guide

High-Performance Computing (HPC)

Supercomputing for Beginners

Provider: ARCCA
Topics: HPC basics, job submission, SLURM
Access: Recorded material
Link: ARCCA Training

What you’ll learn: How to use HPC clusters for large-scale bioinformatics analyses, job scheduling with SLURM.

SLURM – Advanced Topics

Provider: ARCCA
Topics: Job arrays, resource management
Access: Recorded / material
Link: ARCCA Training

Introduction to Parallel Programming (OpenMP & MPI)

Provider: ARCCA
Topics: Parallelisation, shared/distributed memory
Access: Recorded sessions / slides
Link: ARCCA Training

Containers & Reproducibility

Introduction to Containers and Singularity

Provider: ARCCA
Topics: Containerisation, reproducible environments
Access: Recorded sessions + material
Link: ARCCA Training

What you’ll learn: Use containers (Docker/Singularity) to create reproducible computational environments for bioinformatics pipelines.

Machine Learning & AI

Introduction to Machine Learning Applications

Provider: ARCCA
Topics: ML basics, HPC applications
Access: Recorded sessions
Link: ARCCA Training

Basics of Large Language Models – transformers to LLMs

Provider: EMBL-EBI
Topics: Transformer & LLM foundations
Access: Webinar (on-demand)
Link: Webinar

Developing a dataset for LLM projects

Provider: EMBL-EBI
Topics: Data curation for LLMs
Access: Webinar (on-demand)
Link: Webinar

How to Apply LLM Models in Bioinformatics Research (2025)

Provider: OmicsTutorials
Topics: LLMs in bioinformatics
Access: Articles / guides
Link: Category Page

Comprehensive Guides & Best Practices

Comprehensive Bioinformatics Analysis Guide

Provider: OmicsTutorials
Topics: End-to-end overview (data → modeling), pipeline thinking
Access: Article / guide
Link: Read Guide

What you’ll learn: Complete workflow from data acquisition through advanced analysis and modeling.

Things I Wish I Knew When Entering the Bioinformatics Field

Provider: OmicsTutorials
Topics: Variant calling, long-read assembly (Canu), workflow tips
Access: Article / guide
Link: Read Article

What you’ll learn: Practical advice and lessons learned - highly recommended for beginners!

52 Common Mistakes in Bioinformatics and How to Avoid Them

Provider: OmicsTutorials
Topics: Pitfalls incl. alignment/variant calling, parallelising jobs
Access: Article / guide
Link: Read Guide

What you’ll learn: Common pitfalls and how to avoid them - save yourself time and frustration!

Quick Guide Tutorial: Challenges in Big Data and Bioinformatics

Provider: OmicsTutorials
Topics: SAMtools, BEDTools, variant calling basics
Access: Article / guide
Link: Read Guide

Introduction to bioinformatics Sequencing resource

Provider: OmicsTutorials
Topics: Sequencing resources overview
Access: Video tutorial
Link: Watch Video

Recommended Learning Paths

Path 1: Complete Beginner to Variant Calling

Introduction to Linux
Version Control with Git
Programming with Python or R
Data Wrangling and Processing for Genomics
Genome bioinformatics: resequencing & variant calling
Snakemake for Bioinformatics

Path 2: RNA-seq Analysis

Ensure Linux/command line proficiency
Learn R (Programming with R)
Functional Genomics series
Practice with RNA-seq specific tools (see Tools & Setup)

Path 3: Population Genetics & GWAS

Strengthen programming skills (Python or R)
GWAS Catalog course
Analysing linkage disequilibrium
Calculating polygenic scores
Population genetics tutorials

Path 4: Reproducible Research Focus

Version Control with Git
Introduction to Containers
Snakemake or Nextflow workflows
Reproducibility in Bioinformatics
Implement Best Practices

Tips for Self-Study

Learning Strategies

Set aside dedicated time - Block out specific times for learning - Consistency matters more than long sessions

Learn by doing - Work through all the examples - Apply concepts to your own data/projects - Don’t just read - actually run the code!

Take notes - Document commands that work - Note common error messages and solutions - Build your own reference guide

Join communities - Biostars, Stack Overflow for Q&A - Twitter/Mastodon for staying current - Local bioinformatics groups or journal clubs

Track your learning - Use our Analysis Catalogue to track courses - Set goals and milestones - Revisit topics periodically for reinforcement

Staying Current

Bioinformatics evolves rapidly. Ways to keep learning:

Subscribe to journal tables of contents (Nature Methods, Bioinformatics, etc.)
Follow method developers on social media
Attend conferences and webinars
Read preprints (bioRxiv)
Take advanced courses yearly

Next Steps

Implement what you’ve learned with Best Practices
Explore Essential Tools for your workflow
Check Resources for additional databases and communities

--- title: "Tutorials & Workshops" subtitle: "Curated learning resources for bioinformatics" format: html: toc: true toc-depth: 3 --- ## Overview This page contains a comprehensive, searchable catalogue of tutorials, courses, and workshops for bioinformatics. Resources are organized by topic and source, with most being free and self-paced. ::: {.callout-tip} ## How to Use This Catalogue - Use browser search (Ctrl/Cmd+F) to find specific topics - Start with foundational skills (Linux, programming) before diving into advanced genomics - Many courses can be audited for free - look for "Free/self-paced" access - Track your progress using the [Analysis Catalogue Template](best-practices.qmd#analysis-catalogue) ::: --- ## Genomics & NGS {#genomics-ngs} ### Short-Read Sequencing #### Genome bioinformatics: from short- to long-read sequencing **Provider:** EMBL-EBI **Topics:** NGS & long-read sequencing, variant calling, workflows **Access:** Free / self-paced **Link:** [Course Page](https://www.ebi.ac.uk/training/events/genome-bioinformatics-from-short-to-long-read-sequencing) **What you'll learn:** Comprehensive introduction to genome sequencing technologies, transitioning from short-read to long-read approaches, with practical variant calling examples. --- #### Genome bioinformatics: resequencing & variant calling {#variant-calling} **Provider:** EMBL-EBI **Topics:** Short-read variant calling, quality control **Access:** Free / self-paced **Link:** [Course Materials](https://www.ebi.ac.uk/training/materials/genome-bioinformatics-resequencing-and-variant-calling-materials) **What you'll learn:** Hands-on variant calling workflow from raw sequencing data through to filtered, annotated variants. --- #### Data Wrangling and Processing for Genomics {#genomics-data} **Provider:** The Carpentries **Topics:** FASTQ, QC, mapping, variant calling preparation **Access:** Free / self-paced **Link:** [Course Page](https://datacarpentry.org/wrangling-genomics/) **What you'll learn:** Essential skills for processing genomic data including quality control, trimming, alignment, and preparing data for variant calling. --- #### Introduction to Next-Generation Sequencing Technologies {#ngs} **Provider:** OmicsTutorials **Topics:** NGS background **Access:** Video tutorial **Link:** [Watch Video](https://omicstutorials.com/introduction-to-next-generation-sequencing-technologies-video/) --- ### Structural Variants #### Structural Variant detection and comparison (SVs) **Provider:** Physalia Courses **Topics:** SV detection, SV comparison **Access:** Some materials open **Link:** [Course Page](https://www.physalia-courses.org/courses-workshops/svs) **What you'll learn:** Methods for detecting and analyzing structural variations including deletions, duplications, inversions, and translocations. --- ### Variant Annotation & Analysis #### Exploring genotype–phenotype data using Ensembl **Provider:** EMBL-EBI **Topics:** Variant annotation, phenotype links **Access:** Self-paced **Link:** [Course Page](https://www.ebi.ac.uk/training/online/courses/exploring-genotype-phenotype-data-using-the-ensembl-tools) --- #### Variant calling and annotation (FutureLearn) **Provider:** FutureLearn **Topics:** SNV/indel calling, annotation **Access:** Free (register to audit) **Link:** [Course Page](https://www.futurelearn.com/info/courses/making-sense-of-genomic-data-covid-19-web-based-bioinformatics/0/steps/319530) --- ## Population & Complex Trait Genetics ### GWAS & Polygenic Scores #### GWAS Catalog **Provider:** EMBL-EBI **Topics:** GWAS data exploration, variant annotation **Access:** Free / self-paced **Link:** [Course Page](https://www.ebi.ac.uk/training/online/courses/gwas-catalog) **What you'll learn:** How to navigate and interpret GWAS results, understand genome-wide significance, and explore disease-associated variants. --- #### Calculating polygenic scores with the Polygenic Score Catalog Calculator **Provider:** EMBL-EBI **Topics:** PRS / PGS Catalog usage **Access:** Webinar (on-demand) **Link:** [Webinar](https://www.ebi.ac.uk/training/events/calculating-polygenic-scores-polygenic-score-catalog-calculator) **What you'll learn:** How to calculate and interpret polygenic risk scores for complex traits and diseases. --- #### Analysing linkage disequilibrium with Ensembl **Provider:** EMBL-EBI **Topics:** LD analysis, population genetics **Access:** Webinar (on-demand) **Link:** [Webinar](https://www.ebi.ac.uk/training/events/analysing-linkage-disequilibrium-ensembl) --- ### Translational Genomics #### From variant to drug target: using the expanded toolbox **Provider:** EMBL-EBI **Topics:** Translational genomics, target prioritisation **Access:** Free / self-paced **Link:** [Course Page](https://www.ebi.ac.uk/training/online/courses/from-variant-to-drug-target-using-the-expanded-toolbox) **What you'll learn:** How to move from genetic variants identified in GWAS to potential therapeutic targets. --- ## Functional Genomics #### Functional Genomics I–III **Provider:** EMBL-EBI **Topics:** Experimental design, gene regulation, functional assays **Access:** Free / self-paced **Link:** [Course Series](https://www.ebi.ac.uk/training/online/courses/functional-genomics-i-introduction-and-design) **What you'll learn:** Comprehensive introduction to functional genomics including ChIP-seq, ATAC-seq, and other regulatory genomics approaches. --- #### Functional Genomics: From Data to Biological Insight **Provider:** OmicsTutorials **Topics:** Functional genomics overview & tools **Access:** Article / guide **Link:** [Read Article](https://omicstutorials.com/functional-genomics-from-data-to-biological-insight/) --- ## Multi-Omics & Integration #### Introduction to multi-omics data integration and visualisation **Provider:** EMBL-EBI **Topics:** Multi-omics integration, visualization **Access:** Self-paced **Link:** [Course Materials](https://www.ebi.ac.uk/training/materials/introduction-to-multiomics-data-integration-and-visualisation-materials) **What you'll learn:** Methods for integrating genomics, transcriptomics, proteomics, and other omics data types for comprehensive biological insights. --- ## Dementia-Specific Resources #### Data-driven approaches to understanding dementia **Provider:** EMBL-EBI **Topics:** Systems / omics approaches to dementia **Access:** Webinar (on-demand) **Link:** [Webinar](https://www.ebi.ac.uk/training/events/data-driven-approaches-to-understanding-dementia) **What you'll learn:** How genomics, transcriptomics, and other data-driven approaches are being applied to understand dementia mechanisms and identify therapeutic targets. --- ## Workflow Management {#workflows} ### Snakemake #### Snakemake for Bioinformatics **Provider:** Carpentries Incubator **Topics:** Snakemake basics, rules, conda, workflows **Access:** Free / self-paced **Link:** [Course Page](https://carpentries-incubator.github.io/snakemake-novice-bioinformatics) **What you'll learn:** Build reproducible, scalable bioinformatics pipelines using Snakemake. --- #### Galaxy Training: Snakemake Tutorial **Provider:** Galaxy Project **Topics:** Workflow automation, Make → Snakemake transition **Access:** Free / self-paced **Link:** [Tutorial](https://training.galaxyproject.org/training-material/topics/data-science/tutorials/snakemake/tutorial.html) --- #### Reproducible and Scalable Research with Snakemake & Containers **Provider:** SIB Swiss Institute of Bioinformatics **Topics:** Snakemake, Docker/Singularity, reproducibility **Access:** Free materials **Link:** [Training Materials](https://sib-swiss.github.io/containers-snakemake-training) --- ### Nextflow #### Deploying Nextflow pipelines in the cloud **Provider:** EMBL-EBI **Topics:** Nextflow, workflow management **Access:** Webinar (on-demand) **Link:** [Webinar](https://www.ebi.ac.uk/training/events/deploying-nextflow-pipelines-in-the-cloud) --- #### Introduction to Workflow Tool Nextflow **Provider:** ARCCA **Topics:** Workflow management with Nextflow **Access:** Recorded sessions / material **Link:** [ARCCA Training](https://arcca.github.io/index.html) --- ### Reproducibility #### Reproducibility in Bioinformatics **Provider:** Physalia Courses **Topics:** Containers, versioning, Snakemake **Access:** Some slides/materials open **Link:** [Course Page](https://www.physalia-courses.org/courses-workshops/bioinformatics-reproducibility) --- ## Programming Languages ### Python {#python} #### Programming with Python **Provider:** Software Carpentry **Topics:** Python basics **Access:** Free / self-paced **Link:** [Course Page](https://swcarpentry.github.io/python-novice-inflammation/) **What you'll learn:** Python fundamentals including variables, loops, functions, and data structures - essential for bioinformatics scripting. --- #### Plotting and Programming in Python **Provider:** Data Carpentry **Topics:** Python + matplotlib **Access:** Free / self-paced **Link:** [Course Page](https://datacarpentry.org/python-ecology-lesson/) **What you'll learn:** Python programming with a focus on data analysis and visualization using matplotlib and pandas. --- #### Introduction to Python **Provider:** ARCCA **Topics:** Python basics, HPC adaptation **Access:** Recorded sessions **Link:** [ARCCA Training](https://arcca.github.io/index.html) --- #### Advanced Python **Provider:** ARCCA **Topics:** Advanced Python programming **Access:** Recorded sessions **Link:** [ARCCA Training](https://arcca.github.io/index.html) --- ### R Programming {#r-programming} #### Programming with R **Provider:** Software Carpentry **Topics:** R basics **Access:** Free / self-paced **Link:** [Course Page](https://swcarpentry.github.io/r-novice-gapminder/) **What you'll learn:** R fundamentals for data analysis and statistical computing. --- #### R for Reproducible Scientific Analysis **Provider:** Software Carpentry **Topics:** R workflows, reproducibility **Access:** Free / self-paced **Link:** [Course Page](https://swcarpentry.github.io/r-novice-gapminder/) --- ### Databases & SQL #### Databases and SQL **Provider:** Software Carpentry **Topics:** SQL basics, relational queries **Access:** Free / self-paced **Link:** [Course Page](https://swcarpentry.github.io/sql-novice-survey/) **What you'll learn:** Query databases using SQL - useful for working with genomic databases and large datasets. --- ## Version Control {#version-control} #### Version Control with Git **Provider:** Software Carpentry **Topics:** Git, commits, branches, GitHub **Access:** Free / self-paced **Link:** [Course Page](https://swcarpentry.github.io/git-novice/) **What you'll learn:** Essential Git skills for version controlling code and collaborating on projects. **Critical skill for reproducible research.** --- ## Linux & Command Line {#command-line} #### Introduction to Linux with Command Line **Provider:** ARCCA **Topics:** Linux CLI basics, navigation, commands **Access:** Recorded sessions + material **Link:** [ARCCA Training](https://arcca.github.io/index.html) **What you'll learn:** Navigate and use the Linux command line - absolutely essential for bioinformatics work. --- #### Introduction to Linux Shell Scripting **Provider:** ARCCA **Topics:** Writing shell scripts, loops, automation **Access:** Recorded sessions + material **Link:** [ARCCA Training](https://arcca.github.io/index.html) --- #### Comprehensive Guide to Setting up and Using Linux for Bioinformatics Analysis **Provider:** OmicsTutorials **Topics:** Linux setup, shell basics, tooling for bioinformatics **Access:** Article / guide **Link:** [Read Guide](https://omicstutorials.com/comprehensive-guide-to-setting-up-and-using-linux-for-bioinformatics-analysis/) --- #### Mastering Bioinformatics Analysis with FASTA Sequences **Provider:** OmicsTutorials **Topics:** FASTA workflows, Unix/Linux skills **Access:** Article / guide **Link:** [Read Guide](https://omicstutorials.com/mastering-bioinformatics-analysis-with-fasta-sequences-a-biologists-guide-to-unix-and-linux/) --- ## High-Performance Computing (HPC) #### Supercomputing for Beginners **Provider:** ARCCA **Topics:** HPC basics, job submission, SLURM **Access:** Recorded material **Link:** [ARCCA Training](https://arcca.github.io/index.html) **What you'll learn:** How to use HPC clusters for large-scale bioinformatics analyses, job scheduling with SLURM. --- #### SLURM – Advanced Topics **Provider:** ARCCA **Topics:** Job arrays, resource management **Access:** Recorded / material **Link:** [ARCCA Training](https://arcca.github.io/index.html) --- #### Introduction to Parallel Programming (OpenMP & MPI) **Provider:** ARCCA **Topics:** Parallelisation, shared/distributed memory **Access:** Recorded sessions / slides **Link:** [ARCCA Training](https://arcca.github.io/index.html) --- ## Containers & Reproducibility #### Introduction to Containers and Singularity **Provider:** ARCCA **Topics:** Containerisation, reproducible environments **Access:** Recorded sessions + material **Link:** [ARCCA Training](https://arcca.github.io/index.html) **What you'll learn:** Use containers (Docker/Singularity) to create reproducible computational environments for bioinformatics pipelines. --- ## Machine Learning & AI #### Introduction to Machine Learning Applications **Provider:** ARCCA **Topics:** ML basics, HPC applications **Access:** Recorded sessions **Link:** [ARCCA Training](https://arcca.github.io/index.html) --- #### Basics of Large Language Models – transformers to LLMs **Provider:** EMBL-EBI **Topics:** Transformer & LLM foundations **Access:** Webinar (on-demand) **Link:** [Webinar](https://www.ebi.ac.uk/training/events/basics-large-language-models-transformers-llms) --- #### Developing a dataset for LLM projects **Provider:** EMBL-EBI **Topics:** Data curation for LLMs **Access:** Webinar (on-demand) **Link:** [Webinar](https://www.ebi.ac.uk/training/events/developing-a-dataset-for-llm-projects) --- #### How to Apply LLM Models in Bioinformatics Research (2025) **Provider:** OmicsTutorials **Topics:** LLMs in bioinformatics **Access:** Articles / guides **Link:** [Category Page](https://omicstutorials.com/category/bioinformatics/) --- ## Comprehensive Guides & Best Practices #### Comprehensive Bioinformatics Analysis Guide **Provider:** OmicsTutorials **Topics:** End-to-end overview (data → modeling), pipeline thinking **Access:** Article / guide **Link:** [Read Guide](https://omicstutorials.com/comprehensive-bioinformatics-analysis-guide-from-data-acquisition-to-advanced-predictive-modeling-real-time-implementation/) **What you'll learn:** Complete workflow from data acquisition through advanced analysis and modeling. --- #### Things I Wish I Knew When Entering the Bioinformatics Field **Provider:** OmicsTutorials **Topics:** Variant calling, long-read assembly (Canu), workflow tips **Access:** Article / guide **Link:** [Read Article](https://omicstutorials.com/things-i-wish-i-knew-when-entering-the-bioinformatics-field/) **What you'll learn:** Practical advice and lessons learned - highly recommended for beginners! --- #### 52 Common Mistakes in Bioinformatics and How to Avoid Them **Provider:** OmicsTutorials **Topics:** Pitfalls incl. alignment/variant calling, parallelising jobs **Access:** Article / guide **Link:** [Read Guide](https://omicstutorials.com/step-by-step-guide-52-common-mistakes-in-bioinformatics-and-how-to-avoid-them/) **What you'll learn:** Common pitfalls and how to avoid them - save yourself time and frustration! --- #### Quick Guide Tutorial: Challenges in Big Data and Bioinformatics **Provider:** OmicsTutorials **Topics:** SAMtools, BEDTools, variant calling basics **Access:** Article / guide **Link:** [Read Guide](https://omicstutorials.com/quick-guide-tutorial-challenges-in-big-data-and-bioinformatics/) --- #### Introduction to bioinformatics Sequencing resource **Provider:** OmicsTutorials **Topics:** Sequencing resources overview **Access:** Video tutorial **Link:** [Watch Video](https://omicstutorials.com/introduction-to-bioinformatics-sequencing-resource-video-tutorial/) --- ## Recommended Learning Paths ### Path 1: Complete Beginner to Variant Calling 1. [Introduction to Linux](#command-line) 2. [Version Control with Git](#version-control) 3. [Programming with Python](#python) or [R](#r-programming) 4. [Data Wrangling and Processing for Genomics](#genomics-data) 5. [Genome bioinformatics: resequencing & variant calling](#variant-calling) 6. [Snakemake for Bioinformatics](#workflows) --- ### Path 2: RNA-seq Analysis 1. Ensure Linux/command line proficiency 2. Learn R ([Programming with R](#r-programming)) 3. [Functional Genomics series](#functional-genomics) 4. Practice with RNA-seq specific tools (see [Tools & Setup](tools-setup.qmd)) --- ### Path 3: Population Genetics & GWAS 1. Strengthen programming skills (Python or R) 2. [GWAS Catalog course](#gwas) 3. [Analysing linkage disequilibrium](#ld) 4. [Calculating polygenic scores](#prs) 5. Population genetics tutorials --- ### Path 4: Reproducible Research Focus 1. [Version Control with Git](#version-control) 2. [Introduction to Containers](#containers) 3. [Snakemake](#workflows) or [Nextflow](#nextflow) workflows 4. [Reproducibility in Bioinformatics](#reproducibility) 5. Implement [Best Practices](best-practices.qmd) --- ## Tips for Self-Study ::: {.callout-tip} ## Learning Strategies **Set aside dedicated time** - Block out specific times for learning - Consistency matters more than long sessions **Learn by doing** - Work through all the examples - Apply concepts to your own data/projects - Don't just read - actually run the code! **Take notes** - Document commands that work - Note common error messages and solutions - Build your own reference guide **Join communities** - Biostars, Stack Overflow for Q&A - Twitter/Mastodon for staying current - Local bioinformatics groups or journal clubs **Track your learning** - Use our [Analysis Catalogue](best-practices.qmd) to track courses - Set goals and milestones - Revisit topics periodically for reinforcement ::: --- ## Staying Current Bioinformatics evolves rapidly. Ways to keep learning: - Subscribe to journal tables of contents (Nature Methods, Bioinformatics, etc.) - Follow method developers on social media - Attend conferences and webinars - Read preprints (bioRxiv) - Take advanced courses yearly --- ## Next Steps - Implement what you've learned with [Best Practices](best-practices.qmd) - Explore [Essential Tools](tools-setup.qmd) for your workflow - Check [Resources](resources.qmd) for additional databases and communities