Biopython
lamm-mit/scienceclaw
Computational molecular biology library (sequence I/O, alignment, phylogenetics).
ENA REST API for sequences, reads, assemblies, and annotations.
Install Ena Database
$ npx skills add jaechang-hits/SciAgent-Skills --skill ena-database -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install jaechang-hits/SciAgent-Skills ena-database --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/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/genomics-bioinformatics/databases/ena-database .claude/skills/ena-database && 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 "ena-database" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/genomics-bioinformatics/databases/ena-database into .claude/skills/ena-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ena-database", 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/jaechang-hits/SciAgent-Skills/tree/main/skills/genomics-bioinformatics/databases/ena-databaseType 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 jaechang-hits/SciAgent-Skills --skill ena-database -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install jaechang-hits/SciAgent-Skills ena-database --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/genomics-bioinformatics/databases/ena-database .agents/skills/ena-database && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "ena-database" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/genomics-bioinformatics/databases/ena-database into .agents/skills/ena-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ena-database", 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 jaechang-hits/SciAgent-Skills --skill ena-database -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install jaechang-hits/SciAgent-Skills ena-database --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/genomics-bioinformatics/databases/ena-database .cursor/skills/ena-database && 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 "ena-database" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/genomics-bioinformatics/databases/ena-database into .cursor/skills/ena-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ena-database", 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/jaechang-hits/SciAgent-Skills.git --path skills/genomics-bioinformatics/databases/ena-database--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 jaechang-hits/SciAgent-Skills --skill ena-database -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install jaechang-hits/SciAgent-Skills ena-database --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/genomics-bioinformatics/databases/ena-database .gemini/skills/ena-database && 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 "ena-database" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/genomics-bioinformatics/databases/ena-database into .gemini/skills/ena-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ena-database", 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 jaechang-hits/SciAgent-Skills ena-databaseInstalls 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 jaechang-hits/SciAgent-Skills --skill ena-database -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/genomics-bioinformatics/databases/ena-database .github/skills/ena-database && 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 "ena-database" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/genomics-bioinformatics/databases/ena-database into .github/skills/ena-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ena-database", 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 jaechang-hits/SciAgent-Skills --skill ena-database -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install jaechang-hits/SciAgent-Skills ena-database --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/genomics-bioinformatics/databases/ena-database .opencode/skills/ena-database && 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 "ena-database" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/genomics-bioinformatics/databases/ena-database into .opencode/skills/ena-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ena-database", 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
ena-database- GitHub stars
- 371
- Used in
- 1 other repo
- Token cost
- ~5.3k tokens
- SKILL.md length
- 1,133 words
- Files
- 1
- Skills in repo
- 169
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
ENA REST API for sequences, reads, assemblies, and annotations.
- Works in 7 steps: Use tax_tree() over tax_eq() for… → Request only needed fields — reduces… → Prefer JSON format for programmatic… → …
- Tasks that involve Bioinformatics
- SKILL.md covers Overview, When to Use, Prerequisites and Quick Start, plus 9 more sections
- Calls pip; reaches ebi.ac.uk
What it does
Ena Database is an agent skill from jaechang-hits/SciAgent-Skills. ENA REST API for sequences, reads, assemblies, and annotations. Portal API search, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM URLs, taxonomy, cross-refs. For multi-DB Python use bioservices; for NCBI-only use pubmed-database or Biopython Entrez.
Its SKILL.md is about 5.3k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Bioinformatics, Academic paper search and REST APIs. It works with NCBI, PubMed, Python and Biopython. The repository describes itself as: 197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy. RNA-seq, single-cell, drug discovery, proteomics, and more. Powers OmicsHorizon.
When your agent uses it
- Tasks that involve Bioinformatics
- Tasks that involve Academic paper search
- Tasks that involve REST APIs
Example prompts
- “/ena-database”
Requirements
- Python 3
Workflow steps
7 steps, taken from the first numbered list in SKILL.md.
- Use tax_tree() over tax_eq() for organism queries — it includes subspecies and strains automatically
- Request only needed fields — reduces response size and server load significantly
- Prefer JSON format for programmatic access; TSV for large bulk exports (lower overhead)
- Use limit=0 for streaming large result sets directly to file, avoiding memory issues
- Check fastq_ftp and submitted_ftp — some runs have submitted files but no processed FASTQ
- Verify downloads with MD5 — file reports include fastq_md5 for integrity checking
- Anti-pattern: Do not fetch all fields then filter client-side — use query syntax server-side
What it can do on your machine
Read from SKILL.md and the folder at commit 82c862c. 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
Shell commands in SKILL.md call:
pip
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
ebi.ac.uk
Also links to:
ena-docs.readthedocs.ioinsdc.org
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
Ena Database loads about 5.3k tokens when it runs. Until then it costs about 71 tokens; SKILL.md has 1,133 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
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 1,133 words (~5,331 tokens).
“The European Nucleotide Archive (ENA) is EMBL-EBI's comprehensive nucleotide sequence database, encompassing raw sequencing reads, genome assemblies, annotated sequences, and associated metadata. It mirrors and extends INSDC data (GenBank, DDBJ). All access is via REST APIs with no authentication required.”
- name
- ena-database
- license
- Unknown
Files
Just SKILL.md in skills/genomics-bioinformatics/databases/ena-database of jaechang-hits/SciAgent-Skills.
Open the folder on GitHubat commit 82c862c
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 jaechang-hits/SciAgent-Skills, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Ena Database 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 |
|---|---|---|---|---|---|---|
| Ena Database this skilljaechang-hits/SciAgent-Skills | 371 | 1 repos | ~5.3k | Automated safety check: Pass | Custom licence | |
| Biopythonlamm-mit/scienceclaw | 244 | — | ~3.9k | Automated safety check: Pass | Apache-2.0 | |
| Biopythondavila7/claude-code-templates | 32k | 12 repos | ~3.4k | Automated safety check: Pass | MIT | |
| BiopythonK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~4.3k | Automated safety check: Notes | MIT | |
| Bio Entrez FetchGPTomics/bioSkills | 1.2k | 2 repos | ~3.7k | Automated safety check: Pass | MIT | |
| Bio Entrez LinkGPTomics/bioSkills | 1.2k | 2 repos | ~3.8k | Automated safety check: Pass | MIT |
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Related
Categories
Questions about Ena Database
What does Ena Database do?
ENA REST API for sequences, reads, assemblies, and annotations. Ena Database is an agent skill from jaechang-hits/SciAgent-Skills. ENA REST API for sequences, reads, assemblies, and annotations.
When should I use Ena Database?
Ena Database fits situations like: tasks that involve Bioinformatics; tasks that involve Academic paper search; tasks that involve REST APIs.
How do I install Ena Database in Claude Code?
Run `npx skills add jaechang-hits/SciAgent-Skills --skill ena-database -a claude-code`. Or copy the skill folder (skills/genomics-bioinformatics/databases/ena-database in jaechang-hits/SciAgent-Skills) into .claude/skills/ena-database in your project. Claude Code loads it when a task matches its description.
How do I install Ena Database in Codex?
Run `npx skills add jaechang-hits/SciAgent-Skills --skill ena-database -a codex`. Or copy the skill folder (skills/genomics-bioinformatics/databases/ena-database in jaechang-hits/SciAgent-Skills) into .agents/skills/ena-database in your project. Codex loads it when a task matches its description.
Can I use Ena Database 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 jaechang-hits/SciAgent-Skills --skill ena-database -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/ena-database, .gemini/skills/ena-database, .github/skills/ena-database and .opencode/skills/ena-database in your project.
What does Ena Database need to run?
Going by SKILL.md and its folder, Ena Database needs the command-line tools its instructions call (pip). Our summary lists: Python 3.
Does Ena Database access the network?
SKILL.md names 3 domains. In commands or code: ebi.ac.uk; the agent is likely to contact it when it follows the instructions. As links in the text: ena-docs.readthedocs.io and insdc.org. This is read from the text; nothing was executed.
Is Ena Database 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 Ena Database use?
Ena Database has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Ena Database use?
About 5.3k tokens (SKILL.md is roughly 21k 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 Ena Database?
Skills that share tags, products or a category with Ena Database: Biopython (lamm-mit/scienceclaw, 244 stars), Biopython (davila7/claude-code-templates, 32k stars), Biopython (K-Dense-AI/scientific-agent-skills, 48k stars) and Bio Entrez Fetch (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 Ena Database?
jaechang-hits (a GitHub user) maintains it in jaechang-hits/SciAgent-Skills, which has 371 GitHub stars. The repository holds 169 skills in this directory. The repository was last updated on September 29, 2026.
Source: jaechang-hits/SciAgent-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.