bio-read-qc-adapter-trimming SKILL.md skillA
bio-read-qc-adapter-trimming 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-read-qc-adapter-trimming@git:20260621.036f7d0Pins git:20260621.036f7d0 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/adapter-trimming/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260621.036f7d0, committed Jun 21, 2026
- First version recorded
- May 17, 2026
- Size
- 11,618 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Removes sequencing adapters from FASTQ reads with Cutadapt and Trimmomatic, including paired-end read-through, small-RNA 3' adapters, amplicon primers, and anchored/linked adapters. Use when FastQC shows adapter content climbing toward the 3' end, when inserts are shorter than the read length (small-RNA, cfDNA, FFPE), or before assembly/k-mer analysis. For all-in-one trimming use fastp-workflow; for quality/length filtering use quality-filtering.
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: Cutadapt 4.4+, Trimmomatic 0.39+, fastp 0.23+, FastQC 0.12+ Before using code patterns, verify installed versions match. If versions differ: - 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. # Adapter Trimming -- adapter content IS the insert-size distribution Remove adapter sequence that the polymerase read INTO once it ran off the end of a short insert, using Cutadapt (precise, the correctness reference) or Trimmomatic (palindrome mode for paired read-through). **"Trim adapters from my reads"** -> Detect and remove 3' adapter introduced by read-through, then length-filter the survivors. - CLI: `cutadapt -a AGATCGGAAGAGC -A AGATCGGAAGAGC -m 20 -o R1.fq -p R2.fq in_R1.fq in_R2.fq` - All-in-one alternative: `fastp` (PE overlap analysis needs no adapter sequence) -> read-qc/fastp-workflow …
Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-read-qc-adapter-trimming@sha256:b4160a7b97d9aa05The line at the top of this page pins the label git:20260621.036f7d0, 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_vpu5u5pxkr373z2f)
3 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 Jun 21, 2026, about one every 17 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260621.036f7d0 latest | 2026-06-21 | 036f7d0 | 11,618 B | A | view · diff |
| git:20260531.6e617c4 | 2026-05-31 | 6e617c4 | 5,975 B | A | view · diff |
| git:20260517.81511a7 | 2026-05-17 | 81511a7 | 5,976 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 (11618 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_vpu5u5pxkr373z2f GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-read-qc-adapter-trimming GET https://markdownregistry.com/api/v1/blob/b4160a7b97d9aa05cb5a7c701b463850b28721cb4066b41bc8ad03f521ea3ebd
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.