bio-workflows-hic-pipeline
End-to-end Hi-C analysis workflow from contact pairs to compartments, TADs, and loops. Covers cooler matrices, cooltools analysis, and visualization. Use when processing Hi-C data to compartments and TADs.
npx skills add BioTender-max/awesome-bio-agent-skills --skill hic-pipeline --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BWA-MEM2 2.2.1+, cooler 0.9+, cooltools 0.6+, matplotlib 3.8+, numpy 1.26+, pairtools 1.1+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Hi-C Pipeline **"Analyze my Hi-C data from FASTQ to 3D genome features"** → Orchestrate read alignment, contact matrix generation, normalization, TAD calling, loop detection, compartment analysis, and differential interaction testing. Complete workflow for Hi-C chromosome conformation capture analysis. ## Workflow Overview ``` Hi-C FASTQ files | v [1. Alignment & Pairs] --> bwa-mem2 + pairtools | v [2. Matrix Generation] --> cooler | v [3. Normalization] -----> ICE balancing | v [4. Compartments] ------> Eigenvector analysis | v [5. TADs] --------------> Insulation score | v [6. Loops] -------------> Dot calling | v Hi-C features ``` ## Step 1:
- Version Compatibility
- Workflow Overview
- Step 1: Alignment and Pair Processing
- Step 2: Generate Contact Matrix
- Step 3: Normalization (ICE Balancing)
- Step 4: Compartment Analysis
- Step 5: TAD Detection
- Step 6: Loop Calling
- Step 7: Visualization
- Complete Pipeline Script
- Python Analysis Script
- Related Skills
Align Hi-C reads (each end separately, then combine) bwa-mem2 mem -SP5M -t 16 reference.fa reads_R1.fastq.gz | \ pairtools parse --min-mapq 40 --walks-policy 5unique \ pairtools sort --nproc 16 --tmpdir ./tmp | \ pairtools dedup --nproc-in 8 --nproc-out 8 \ pairtools split --nproc-in 8 --output-pairs sample.pairs.gz bwa-mem2 mem -SP5M -t 16 reference.fa \ reads_R1.fastq.gz reads_R2.fastq.gz | \ pairtools sort | \ pairtools dedup --mark-dups --output-stats stats.txt | \
What does the bio-workflows-hic-pipeline skill do?
End-to-end Hi-C analysis workflow from contact pairs to compartments, TADs, and loops. Covers cooler matrices, cooltools analysis, and visualization. Use when processing Hi-C data to compartments and TADs.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill hic-pipeline --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.