Bioinformatics — Gateway to 400+ genomics and computational biology skills
Bioinformatics — Gateway to 400+ genomics and computational biology skills
Start with meaning, then move to detail.
This lesson explains Bioinformatics — Gateway to 400+ genomics and computational biology skills as part of extending Hermes and connecting external tools. You will learn what it does, when it matters, and the smallest safe test that proves it works.
If you are new, do not memorize names. Focus on three questions: what problem does this solve, what access does it need, and how can you verify the result?
For practice, inspect the first example, identify its effects, run it on test data, and compare the result with the source claim.
For advanced readers, inspect Skill metadata, Reference: full SKILL.md, Sources, then verify failure modes and version compatibility.
Complete installation and one successful task before adding new capabilities.
A clear outcome before you read.
- Understand Bioinformatics — Gateway to 400+ genomics and computational biology skills without assumed prior knowledge.
- Separate the source description from what still needs testing in your environment.
- Read the first command and identify its inputs and outputs before copying it.
Short definitions before the details.
- Gateway
- The process that connects Hermes to channels such as Telegram or Discord and routes messages.
- Skill
- An instruction bundle that teaches Hermes a repeatable workflow without necessarily adding an external service.
Gateway to 400+ genomics and computational biology skills
What does the source say, and in what order?
- 01Skill metadata
Start here to understand the core idea or structure.
- 02Reference: full SKILL.md
Read this after the foundation, then connect it to the previous step.
- 03Sources
Read this after the foundation, then connect it to the previous step.
- 04How to fetch and use a skill
Read this after the foundation, then connect it to the previous step.
- 05Skill Index by Domain
Read this after the foundation, then connect it to the previous step.
- 06Sequence Fundamentals
Read this after the foundation, then connect it to the previous step.
- 07Read QC & Alignment
Read this after the foundation, then connect it to the previous step.
- 08Variant Calling & Annotation
Read this after the foundation, then connect it to the previous step.
- 09Differential Expression (Bulk RNA-seq)
Read this after the foundation, then connect it to the previous step.
- 10Single-Cell RNA-seq
Finish here to verify the result and special cases.
Copy only after you understand the effect.
# bioSkills (reference material)
git clone --depth 1 https://github.com/GPTomics/bioSkills.git /tmp/bioSkills
# ClawBio (runnable pipelines)
git clone --depth 1 https://github.com/ClawBio/ClawBio.git /tmp/ClawBio# bioSkills — each skill is at: <category>/<skill-name>/SKILL.md
cat /tmp/bioSkills/variant-calling/gatk-variant-calling/SKILL.md
# ClawBio — each skill is at: skills/<skill-name>/
cat /tmp/ClawBio/skills/pharmgx-reporter/README.md# Python
pip install biopython pysam cyvcf2 pybedtools pyBigWig scikit-allel anndata scanpy mygene
# R/Bioconductor
Rscript -e 'BiocManager::install(c("DESeq2","edgeR","Seurat","clusterProfiler","methylKit"))'
# CLI tools (Ubuntu/Debian)
sudo apt install samtools bcftools ncbi-blast+ minimap2 bedtools
# CLI tools (macOS)
brew install samtools bcftools blast minimap2 bedtools
# Or via Conda (recommended for reproducibility)
conda install -c bioconda samtools bcftools blast minimap2 bedtools fastp kraken2Read the first command and identify its inputs and outputs before copying it.
Match every command to your installed Hermes version, review the files and accounts it can reach, and use non-sensitive data for the first test. If this explanation differs from the source, the official source wins.