Bioinformatics Engineer Learning Roadmap

System Administration

• Linux 鳥哥的 Linux 私房菜
• UNIX
• Windows Server 2025

Programming Languages

• Java
• Perl
• PHP
• Python
• R
• MySQL
• JavaScript
• Julia
• Rust
• Bash/Shell scripting (essential for automation)
• Go (for high-performance applications)

Bioinformatics Tools

• GATK (Genome Analysis Toolkit)
• BWA (Burrows-Wheeler Aligner)
• VCFTools
• IGV (Integrative Genomics Viewer)
• STAR (Spliced Transcripts Alignment to a Reference)
• SAMtools
• Picard
• QIIME2 (Quantitative Insights into Microbial Ecology)
• HISAT2 (High-performance alignment tool for RNA-Seq)
• FastQC (Quality control for sequencing data)
• Trimmomatic (Adapter and quality trimming for sequencing reads)
• Bowtie2 (Fast and memory-efficient aligner)
• DESeq2 (Differential gene expression analysis in R)
• EdgeR (Differential expression analysis of RNA-Seq data)
• StringTie (Transcript assembly and quantification)
• Kraken2 (Ultrafast metagenomics classifier)
• MetaPhlAn (Taxonomic profiling for metagenomics)
• HUMAnN (Functional profiling of microbial communities)
• BLAST (Basic Local Alignment Search Tool)
• Clustal Omega (Multiple sequence alignment tool)
• MUSCLE (Multiple sequence alignment)
• PhyML (Phylogenetic tree construction)
• MEGA (Molecular Evolutionary Genetics Analysis software)
• PLINK (Genome-wide association studies analysis)
• ANNOVAR (Functional annotation of genetic variants)

Bioinformatics Analyses

• RNA-Seq analysis
• WGS (Whole Genome Sequencing) and WES (Whole Exome Sequencing)
• 16S rRNA microbial community analysis
• Metagenomics
• Pathway analysis
• Unix/Linux-based bioinformatics pipelines
• Cluster computing with PBS or SLURM

Molecular Docking and Dynamic Simulation

• Proficiency in molecular docking software
  • AutoDock
• Proficiency in dynamic simulation software
  • GROMACS
  • AMBER
  • CHARMM

Version Control and Code Deployment

• Git (essential for version control)
• GitHub (code hosting and collaboration)
• GitLab
• Other code distribution/deployment tools (e.g., Bitbucket, Jenkins, or CI/CD platforms)

Containerization Technology

• Docker (containerization for reproducibility)
• Singularity (containerization for HPC environments)

Workflow Development Tools

• CWL (Common Workflow Language)
• WDL (Workflow Description Language)
• Nextflow
• Snakemake

Web Development and Database Management

• R/Shiny (interactive web applications for data visualization)
• JavaScript
• Django (Python web framework)
• Laravel (PHP web framework)
• Ruby on Rails (RoR)
• Web development basics (HTML, CSS, REST APIs)
• Database management (SQL, NoSQL, relational database design)

Machine Learning

• Experience with machine learning algorithms and frameworks
  • TensorFlow/PyTorch/Scikit-learn
  • Application of ML in omics data (e.g., gene expression analysis, feature selection)

Cloud Environment Expertise

• AWS (Amazon Web Services)
  • EC2 (Elastic Compute Cloud)
  • S3 (Simple Storage Service)
  • Batch (job orchestration)
• Google Cloud Platform (GCP)
  • BigQuery
  • Dataflow
• Azure (Microsoft cloud platform)
• Cloud-native workflow orchestration (e.g., Cromwell, Argo)