Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-workflows-hic-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

Hi-C contact map generation, normalization, TAD/loop calling.

OpenClawNanoClawAnalysisReproductionbio-workflows-hic-pipeline🧠 bioos extended suitebioos extended bioinformatics suitehi

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-workflows-hic-pipeline

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Complete workflow for Hi-C chromosome conformation capture analysis.

Source Doc

Excerpt From SKILL.md

Alternative: align both ends

bwa-mem2 mem -SP5M -t 16 reference.fa
reads_R1.fastq.gz reads_R2.fastq.gz |
pairtools parse --min-mapq 40 --walks-policy 5unique
--max-inter-align-gap 30 --chroms-path reference.genome |
pairtools sort |
pairtools dedup --mark-dups --output-stats stats.txt |
pairtools split --output-pairs sample.pairs.gz


**QC Checkpoint:** Check pair statistics
- Valid pairs >50% of total
- Cis pairs >70% (intra-chromosomal)
- Duplicate rate reasonable

## Create cooler file at multiple resolutions

cooler cload pairs \
    -c1 2 -p1 3 -c2 4 -p2 5 \
    reference.genome:1000 \
    sample.pairs.gz \
    sample.1000.cool

## Multi-resolution (mcool)

cooler zoomify sample.1000.cool \
    -r 1000,2000,5000,10000,25000,50000,100000,250000,500000,1000000 \
    -o sample.mcool

Use cases

Use bio-workflows-hic-pipeline for genomics and bioinformatics workflows.
Apply bio-workflows-hic-pipeline to sequencing, variant, or omics analysis tasks.