bio-alignment-amplicon-clipping SKILL.md skillA
bio-alignment-amplicon-clipping 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-alignment-amplicon-clipping@git:20260712.2ff971bPins git:20260712.2ff971b 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/alignment-amplicon-clipping/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260712.2ff971b, committed Jul 12, 2026
- First version recorded
- May 17, 2026
- Size
- 8,993 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints.
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: samtools 1.19+, pysam 0.22+ 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. # Alignment Amplicon Clipping **"Trim primer-derived bases from amplicon BAM"** -> Soft- or hard-clip the 5' primer footprint after alignment using a primer BED, then repair fixmate/MD/NM tags. - CLI: `samtools ampliconclip -b primers.bed input.bam -o clipped.bam` (since samtools 1.11) - Alternative: `iVar trim`, `BAMClipper`, `fgbio ClipBam` ## Why Primer Trimming After Alignment Amplicon panels (SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, fusion panels, 16S rRNA) use designed PCR primers for enrichment. Primer-derived bases at read 5' ends do NOT reflect biological sequence -- they reflect the primer template. Without trimming: - False reference confirmation at primer footprint positions. …
Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-alignment-amplicon-clipping@sha256:e87d3d0b41ad310bThe line at the top of this page pins the label git:20260712.2ff971b, 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_vnqpqbhdm2utlwb2)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between May 17, 2026 and Jul 12, 2026, about one every 28 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260712.2ff971b latest | 2026-07-12 | 2ff971b | 8,993 B | A | view · diff |
| git:20260528.89ddef6 | 2026-05-28 | 89ddef6 | 8,228 B | A | view · diff |
| git:20260517.81511a7 | 2026-05-17 | 81511a7 | 8,197 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 (8993 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_vnqpqbhdm2utlwb2 GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-alignment-amplicon-clipping GET https://markdownregistry.com/api/v1/blob/e87d3d0b41ad310bf9461110b57a6b060b928a8a8fc8c2be391e5d84c5c7ff0a
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.
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