Skills

A curated collection of technical skills and tutorials for bioinformatics, organized by topic. All posts are hands-on guides with practical examples.

Version Control & Git

1. The Evolution of Version Control - Git's Role in Reproducible Bioinformatics (Part 1)
2. The Evolution of Version Control - CI/CD in bioinformatics (Part 2)
3. Running GitHub Actions Locally with act: 5x Faster Development

Containers & Docker

1. Containers in Bioinformatics: Community Tooling and Efficient Docker Building
2. Containers on HPC: From Docker to Singularity and Apptainer
3. Docker Out of Docker: Running Interactive Web Applications for Data Analysis

Package Management & Environment Setup

1. Pixi - New conda era
2. Upgrade Your Shell: From Bash to Zsh for a Better Terminal Experience
3. Setting Up a Local Nextflow Training Environment with Code-Server and HPC

Nextflow & Workflow Management

1. RIVER - A Web Application to Run Nf-Core
2. How to Migrate from In-House Pipelines to Enterprise-Level Workflows: A Proven 3-Step Validation Framework
3. Bioinformatics Cost Optimization for Computing Resources Using Nextflow (Part 1)
4. Bioinformatics Cost Optimization For Input Using Nextflow (Part 2)

Variant Calling & NGS Pipelines

1. Building a Reproducible GATK Variant Calling Bash Workflow with Pixi (Part 1) - Academic proof-of-concept implementation
2. From Bash to Nextflow: GATK Best Practice With Nextflow (Part 2) - MD5 validation and scientific equivalence testing
3. Variant Calling at Production Scale: HPC Deployment and Performance Optimization (Part 3) - SLURM, resource optimization, and scaling to 100+ samples

Slurm & HPC Clusters

1. Building a Slurm HPC Cluster (Part 1) - Single Node Setup and Fundamentals
2. Building a Slurm HPC Cluster (Part 2) - Scaling to Production with Ansible
3. Building a Slurm HPC Cluster (Part 3) - Administration and Best Practices

CI/CD & Testing

1. The Evolution of Version Control - CI/CD in bioinformatics (Part 2)
2. Running GitHub Actions Locally with act: 5x Faster Development
3. Bioinformatics Workflow Template: Standardizing Python Pipelines with Modular Design

Machine Learning & Data Analysis

1. Introduction to AI/ML in Bioinformatics: Classification Models & Evaluation
2. Machine Learning in Bioinformatics Part 1: Building KNN from Scratch

Data Management & Cloud Storage

1. Working with Remote Files using bcftools and samtools (HTSlib) - S3, HTTP, and cloud file access

Performance Optimization

1. Unix Pipes in Bioinformatics: How Streaming Data Reduces Memory and Storage
2. Bioinformatics Cost Optimization for Computing Resources Using Nextflow (Part 1)
3. Bioinformatics Cost Optimization For Input Using Nextflow (Part 2)