- Linux 鳥哥的 Linux 私房菜
- UNIX
- Windows Server 2025
- Java
- Perl
- PHP
- Python
- R
- MySQL
- JavaScript
- Julia
- Rust
- Bash/Shell scripting (essential for automation)
- Go (for high-performance applications)
- 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)
- 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
- Proficiency in molecular docking software
- Proficiency in dynamic simulation software
- Git (essential for version control)
- GitHub (code hosting and collaboration)
- GitLab
- Other code distribution/deployment tools (e.g., Bitbucket, Jenkins, or CI/CD platforms)
- Docker (containerization for reproducibility)
- Singularity (containerization for HPC environments)
- 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)
- Experience with machine learning algorithms and frameworks
- TensorFlow/PyTorch/Scikit-learn
- Application of ML in omics data (e.g., gene expression analysis, feature selection)
- AWS (Amazon Web Services)
- Google Cloud Platform (GCP)
- Azure (Microsoft cloud platform)
- Cloud-native workflow orchestration (e.g., Cromwell, Argo)