Bio Read Qc Adapter Trimming
GPTomics/bioSkills
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.
Agent skill
Bio Read Qc Adapter Trimming
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic.
No licenceAuto-check passed
Install Bio Read Qc Adapter Trimming
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-qc-adapter-trimming -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-read-qc-adapter-trimming --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio-read-qc-adapter-trimming .claude/skills/bio-read-qc-adapter-trimming && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "bio-read-qc-adapter-trimming" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-qc-adapter-trimming into .claude/skills/bio-read-qc-adapter-trimming/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-read-qc-adapter-trimming", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-qc-adapter-trimmingType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-qc-adapter-trimming -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-read-qc-adapter-trimming --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bio-read-qc-adapter-trimming .agents/skills/bio-read-qc-adapter-trimming && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bio-read-qc-adapter-trimming" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-qc-adapter-trimming into .agents/skills/bio-read-qc-adapter-trimming/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-read-qc-adapter-trimming", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-qc-adapter-trimming -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-read-qc-adapter-trimming --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bio-read-qc-adapter-trimming .cursor/skills/bio-read-qc-adapter-trimming && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "bio-read-qc-adapter-trimming" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-qc-adapter-trimming into .cursor/skills/bio-read-qc-adapter-trimming/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-read-qc-adapter-trimming", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git --path skills/bio-read-qc-adapter-trimming--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-qc-adapter-trimming -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-read-qc-adapter-trimming --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bio-read-qc-adapter-trimming .gemini/skills/bio-read-qc-adapter-trimming && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "bio-read-qc-adapter-trimming" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-qc-adapter-trimming into .gemini/skills/bio-read-qc-adapter-trimming/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-read-qc-adapter-trimming", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-read-qc-adapter-trimmingInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-qc-adapter-trimming -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bio-read-qc-adapter-trimming .github/skills/bio-read-qc-adapter-trimming && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "bio-read-qc-adapter-trimming" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-qc-adapter-trimming into .github/skills/bio-read-qc-adapter-trimming/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-read-qc-adapter-trimming", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-qc-adapter-trimming -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-read-qc-adapter-trimming --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bio-read-qc-adapter-trimming .opencode/skills/bio-read-qc-adapter-trimming && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "bio-read-qc-adapter-trimming" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-qc-adapter-trimming into .opencode/skills/bio-read-qc-adapter-trimming/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-read-qc-adapter-trimming", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
bio-read-qc-adapter-trimming- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~1.5k tokens
- SKILL.md length
- 221 words
- Files
- 3
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic.
- FastQC shows adapter contamination
- SKILL.md covers Version Compatibility, Common Adapter Sequences, Cutadapt and Trimmomatic, plus 3 more sections
- Runs Shell scripts from its folder
- Before alignment of short reads
What it does
Bio Read Qc Adapter Trimming is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequences. Use when FastQC shows adapter contamination or before alignment of short reads.
Its SKILL.md is about 1.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/trim_adapters.sh` and `usage-guide.md`).
The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- FastQC shows adapter contamination
- Before alignment of short reads
Example prompts
- “/bio-read-qc-adapter-trimming”
Requirements
- A Bash shell
What it can do on your machine
Read from SKILL.md and the folder at commit b1f9b6e. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships script files (Shell), which the agent can run.
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Bio Read Qc Adapter Trimming loads about 1.5k tokens when it runs. Until then it costs about 71 tokens; SKILL.md has 221 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
Without a licence we can't republish the file, so here is its outline and opening line. It has 221 words (~1,494 tokens).
“Reference examples tested with: FastQC 0.12+, Trimmomatic 0.39+, cutadapt 4.4+, fastp 0.23+”
- name
- bio-read-qc-adapter-trimming
- tool_type
- cli
- primary_tool
- cutadapt
Files
SKILL.md and 2 other files in skills/bio-read-qc-adapter-trimming of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/trim_adapters.sh
- usage-guide.md
Open the folder on GitHubat commit b1f9b6e
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in FreedomIntelligence/OpenClaw-Medical-Skills, which our catalogue first saw on October 9, 2026.
Compare with similar skills
Bio Read Qc Adapter Trimming next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Bio Read Qc Adapter Trimming this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.5k | Automated safety check: Pass | None | |
| Bio Read Qc Adapter TrimmingGPTomics/bioSkills | 1.2k | 1 repos | ~2.9k | Automated safety check: Pass | MIT | |
| Bio Write SequencesGPTomics/bioSkills | 1.2k | 3 repos | ~2.1k | Automated safety check: Pass | MIT | |
| Bio Read SequencesGPTomics/bioSkills | 1.2k | 1 repos | ~3.5k | Automated safety check: Pass | MIT | |
| Bio Alignment TrimmingGPTomics/bioSkills | 1.2k | 2 repos | ~5.9k | Automated safety check: Pass | MIT | |
| Bio Fastq QualityGPTomics/bioSkills | 1.2k | 1 repos | ~3.6k | Automated safety check: Pass | MIT |
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Bio Write Sequences
GPTomics/bioSkills
Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO.
Bio Read Sequences
GPTomics/bioSkills
Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) with Biopython Bio.SeqIO, choosing between streaming, in-memory, and on-disk-indexed access.
Bio Alignment Trimming
GPTomics/bioSkills
Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal.
Bio Fastq Quality
GPTomics/bioSkills
Work with FASTQ quality scores using Biopython - access Phred scores, filter and trim by quality, compute per-position profiles, and convert between Sanger/Phred+33, Solexa, and Illumina/Phred+64…
Bio Workflows Fastq To Variants
GPTomics/bioSkills
Orchestrates the end-to-end germline short-variant pipeline from FASTQ to a filtered, normalized, benchmarked VCF, chaining QC/trim, BWA-MEM2 alignment, duplicate marking, optional BQSR, calling…
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Questions about Bio Read Qc Adapter Trimming
What does Bio Read Qc Adapter Trimming do?
Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Bio Read Qc Adapter Trimming is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic.
When should I use Bio Read Qc Adapter Trimming?
Bio Read Qc Adapter Trimming fits situations like: fastQC shows adapter contamination; before alignment of short reads.
How do I install Bio Read Qc Adapter Trimming in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-qc-adapter-trimming -a claude-code`. Or copy the skill folder (skills/bio-read-qc-adapter-trimming in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-read-qc-adapter-trimming in your project. Claude Code loads it when a task matches its description.
How do I install Bio Read Qc Adapter Trimming in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-qc-adapter-trimming -a codex`. Or copy the skill folder (skills/bio-read-qc-adapter-trimming in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-read-qc-adapter-trimming in your project. Codex loads it when a task matches its description.
Can I use Bio Read Qc Adapter Trimming in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-qc-adapter-trimming -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-read-qc-adapter-trimming, .gemini/skills/bio-read-qc-adapter-trimming, .github/skills/bio-read-qc-adapter-trimming and .opencode/skills/bio-read-qc-adapter-trimming in your project.
What does Bio Read Qc Adapter Trimming need to run?
Going by SKILL.md and its folder, Bio Read Qc Adapter Trimming needs a shell for the scripts in its folder. Our summary lists: A Bash shell.
Does Bio Read Qc Adapter Trimming access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Bio Read Qc Adapter Trimming safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Bio Read Qc Adapter Trimming use?
No licence was found for Bio Read Qc Adapter Trimming or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Read Qc Adapter Trimming use?
About 1.5k tokens (SKILL.md is roughly 6k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Bio Read Qc Adapter Trimming?
Skills that share tags, products or a category with Bio Read Qc Adapter Trimming: Bio Read Qc Adapter Trimming (GPTomics/bioSkills, 1.2k stars), Bio Write Sequences (GPTomics/bioSkills, 1.2k stars), Bio Read Sequences (GPTomics/bioSkills, 1.2k stars) and Bio Alignment Trimming (GPTomics/bioSkills, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Read Qc Adapter Trimming?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,053 GitHub stars. The repository holds 279 skills in this directory. The repository was last updated on July 21, 2026.
Source: FreedomIntelligence/OpenClaw-Medical-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.