bio-workflows-atacseq-pipeline SKILL.md skillA
bio-workflows-atacseq-pipeline from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-workflows-atacseq-pipeline@git:20260719.44d7640Pins git:20260719.44d7640 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
- Path
skills/atacseq-pipeline/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260719.44d7640, committed Jul 19, 2026
- First version recorded
- May 31, 2026
- Size
- 16,591 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Orchestrates the end-to-end bulk ATAC-seq pipeline from FASTQ to differential accessibility and TF footprints, chaining Nextera-aware fastp QC, Bowtie2 alignment, chrM removal, dedup, a single Tn5 +4/-5 shift, MACS3 peak calling, Corces fixed-width consensus, DiffBind/csaw differential accessibility, and TOBIAS footprinting. Use when committing the reference build + blacklist once, recognizing ATAC has NO input control (the shift-extend model IS the background), applying the Tn5 shift exactly…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility
Reference examples tested with: Bowtie2 2.5.3+, MACS3 3.0+, Genrich 0.6+, bedtools 2.31+, deepTools 3.5+ (alignmentSieve), fastp 0.23+, samtools 1.19+, DiffBind 3.12+, TOBIAS 0.16+
Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
- 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.
Note: `macs3 callpeak -f BAMPE` uses real fragment lengths and IGNORES `--shift/--extsize/--nomodel`; the cut-site style needs `-f BAM`/`-f BED` on Tn5-shifted reads. `alignmentSieve --ATACshift` applies the +4/-5 shift once. ENCODE ATAC-seq v3 and v4 QC thresholds are not interchangeable. Confirm in-tool before quoting.
# ATAC-seq Pipeline
**"Run ATAC-seq from FASTQ to differential accessibility and footprints"** -> Chain QC/trim, alignment, chrM removal, dedup, a single Tn5 shift, peak calling, fixed-width consensus, differential accessibility, and footprinting.
…Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-workflows-atacseq-pipeline@sha256:29d5c5675fcc092dThe line at the top of this page pins the label git:20260719.44d7640, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_dqyfa6h3dzyspmir)
1 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 5 versions of this file, between May 31, 2026 and Jul 19, 2026, about one every 12 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260719.44d7640 latest | 2026-07-19 | 44d7640 | 16,591 B | A | view · diff |
| git:20260712.2ff971b | 2026-07-12 | 2ff971b | 16,596 B | A | view · diff |
| git:20260628.aa12f9b | 2026-06-28 | aa12f9b | 11,788 B | A | view · diff |
| git:20260621.036f7d0 | 2026-06-21 | 036f7d0 | 11,761 B | A | view · diff |
| git:20260531.6e617c4 | 2026-05-31 | 6e617c4 | 11,560 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (16591 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-10-18 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_dqyfa6h3dzyspmir GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-workflows-atacseq-pipeline GET https://markdownregistry.com/api/v1/blob/29d5c5675fcc092df206eaf58d21cb20fcf904ab50e5d3e0187cc45479242f7b
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.