pipeline-hic skillA
pipeline-hic is agent-read markdown (skill) from ammawla/encode-toolkit: Execute ENCODE Hi-C pipeline from FASTQ to contact matrices and loop calls. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing Hi-C data, generating contact matrices, or calling loops. Trigger on: Hi-C pipeline, chromatin conformation, contact matrix, loop calling, TAD detection, Juicer, HiCCUPS, 3D genome..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
# ENCODE Hi-C Pipeline: FASTQ to Contact Matrices and Loops
## When to Use
- User wants to run a Hi-C processing pipeline from FASTQ to contact matrices and loop calls
- User asks about "Hi-C pipeline", "contact matrix", "loop calling", "Juicer", "HiCCUPS", or "TAD detection"
- User needs to process Hi-C data for 3D genome structure analysis
- Example queries: "process my Hi-C FASTQs", "generate contact matrices from Hi-C", "call chromatin loops with HiCCUPS"
Execute the ENCODE Hi-C pipeline for chromatin conformation capture data,
producing multi-resolution contact matrices and loop calls.
## Pipeline Overview
```
FASTQ -> FastQC (raw reads)
-> bwa mem -SP5M (both mates in one call) -> {sample}.paired.bam
-> pairtools parse -> sort -> dedup -> select UU
|
+-> Juicer pre -> .hic -> HiCCUPS -> loops (BEDPE)
|
+-> cooler cload + zoomify -> .mcool
```
### Not run by this workflow
Adapter trimming, TAD calling, A/B compartment calling, and every cooltools
analysis are outside this workflow. They are documented as manual, optional
steps only: trimming in `references/01-qc-trimming.md`, distance decay and
…Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/pipeline-hic@git:20260921.4ba10c6mdr add ammawla/encode-toolkit/pipeline-hic@sha256:0181f164858afd5bPin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_uds6xmvyxdhv2ixj)
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Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260921.4ba10c6 latest | 2026-09-21 | 4ba10c6 | 21,796 B | A | view · diff |
| git:20260921.ed45b8d | 2026-09-21 | ed45b8d | 21,751 B | A | view · diff |
| git:20260920.6050003 | 2026-09-20 | 6050003 | 21,704 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 20,054 B | A | view · diff |
| git:20260920.bc6cada | 2026-09-20 | bc6cada | 15,575 B | A | view |
Audit of the latest version
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Source
ammawla/encode-toolkit · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_uds6xmvyxdhv2ixj GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/pipeline-hic GET https://markdownregistry.com/api/v1/blob/0181f164858afd5beb3fe5b8f665e132c86f8013d688455c1a6476991bb4c0ff
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