Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
A skill your agent uses when working on bioinformatics workflows such as alignment, variant calling, phylogenetics, or protein-structure analysis, especially across BLAST, minimap2, samtools…
$ npx skills add ZimoLiao/scholaraio --skill bioinformatics -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install ZimoLiao/scholaraio bioinformatics --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/ZimoLiao/scholaraio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.claude/skills/bioinformatics .claude/skills/bioinformatics && 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 "bioinformatics" agent skill from https://github.com/ZimoLiao/scholaraio/tree/main/.claude/skills/bioinformatics into .claude/skills/bioinformatics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioinformatics", 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/ZimoLiao/scholaraio/tree/main/.claude/skills/bioinformaticsType 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 ZimoLiao/scholaraio --skill bioinformatics -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install ZimoLiao/scholaraio bioinformatics --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ZimoLiao/scholaraio.git skills-src && mkdir -p .agents/skills && cp -r skills-src/.claude/skills/bioinformatics .agents/skills/bioinformatics && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bioinformatics" agent skill from https://github.com/ZimoLiao/scholaraio/tree/main/.claude/skills/bioinformatics into .agents/skills/bioinformatics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioinformatics", 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 ZimoLiao/scholaraio --skill bioinformatics -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install ZimoLiao/scholaraio bioinformatics --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ZimoLiao/scholaraio.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/.claude/skills/bioinformatics .cursor/skills/bioinformatics && 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 "bioinformatics" agent skill from https://github.com/ZimoLiao/scholaraio/tree/main/.claude/skills/bioinformatics into .cursor/skills/bioinformatics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioinformatics", 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/ZimoLiao/scholaraio.git --path .claude/skills/bioinformatics--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 ZimoLiao/scholaraio --skill bioinformatics -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install ZimoLiao/scholaraio bioinformatics --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ZimoLiao/scholaraio.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/.claude/skills/bioinformatics .gemini/skills/bioinformatics && 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 "bioinformatics" agent skill from https://github.com/ZimoLiao/scholaraio/tree/main/.claude/skills/bioinformatics into .gemini/skills/bioinformatics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioinformatics", 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 ZimoLiao/scholaraio bioinformaticsInstalls 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 ZimoLiao/scholaraio --skill bioinformatics -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/ZimoLiao/scholaraio.git skills-src && mkdir -p .github/skills && cp -r skills-src/.claude/skills/bioinformatics .github/skills/bioinformatics && 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 "bioinformatics" agent skill from https://github.com/ZimoLiao/scholaraio/tree/main/.claude/skills/bioinformatics into .github/skills/bioinformatics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioinformatics", 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 ZimoLiao/scholaraio --skill bioinformatics -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install ZimoLiao/scholaraio bioinformatics --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ZimoLiao/scholaraio.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/.claude/skills/bioinformatics .opencode/skills/bioinformatics && 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 "bioinformatics" agent skill from https://github.com/ZimoLiao/scholaraio/tree/main/.claude/skills/bioinformatics into .opencode/skills/bioinformatics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioinformatics", 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.
bioinformaticsA skill your agent uses when working on bioinformatics workflows such as alignment, variant calling, phylogenetics, or protein-structure analysis, especially across BLAST, minimap2, samtools…
Bioinformatics is an agent skill from ZimoLiao/scholaraio. Use when working on bioinformatics workflows such as alignment, variant calling, phylogenetics, or protein-structure analysis, especially across BLAST, minimap2, samtools, bcftools, MAFFT, IQ-TREE, or ESMFold.
Its SKILL.md is about 1.4k 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. The repository describes itself as: Scholar All-In-One: A research infrastructure for AI agents. The licence is MIT.
5 steps, taken from the first numbered list in SKILL.md.
Read from SKILL.md and the folder at commit 777628b. It shows what the files ask for, not the result of running them.
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.
Shell commands in SKILL.md call:
pipcondaFrom the folder's file list and the shell code blocks in SKILL.md.
No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.
From URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Bioinformatics loads about 1.4k tokens when it runs. Until then it costs about 56 tokens; SKILL.md has 321 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.
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.
The full file from ZimoLiao/scholaraio at commit 777628b, republished under its MIT licence (© ZimoLiao). 321 words, ~1,350 tokens.
.claude/skills/bioinformatics/SKILL.md (or your agent's skills folder).用生物信息学工具链做序列比对、变异检测、系统发育和蛋白质结构分析。
本 skill 故意保持轻量:
scholaraio toolrefBioinformatics 不是单一程序,而是一组工具链。agent 必须先判断自己在用哪一个子工具,再决定怎么查。
默认顺序:
toolref show bioinformatics <program> ... 或 search --program <program> 查对应程序toolref 覆盖不全,agent 应先回退该工具的官方手册或 README,再继续任务toolref这意味着:
bioinformatics skill 负责先分流,再选工具toolref 负责各子工具的接口细节# 核心工具(conda bioconda 频道)
conda install -c bioconda minimap2 mafft iqtree bcftools samtools blast
# Python 库
pip install biopython py3Dmol pycirclize toytree matplotlib seaborn pandas
# 蛋白质结构预测(需 GPU)
pip install fair-esm
# 数据获取
pip install ncbi-datasets-cli验证:minimap2 --version、samtools --version、blastn -version 均应正常输出。
适合:
不适合:
当 agent 不确定子命令、选项、参数含义时,先查 toolref。
常用查法:
scholaraio toolref show bioinformatics samtools sort
scholaraio toolref show bioinformatics bcftools manual
scholaraio toolref show bioinformatics minimap2 manual
scholaraio toolref show bioinformatics blast blastn
scholaraio toolref search bioinformatics bootstrap tree --program iqtree推荐习惯:
如果遇到覆盖缺口:
toolref 覆盖不足toolref| 工具 | 功能 | 何时用 |
|---|---|---|
| BLAST | 序列相似性搜索 | 查找同源序列、注释未知基因 |
| minimap2 | 序列比对 | 组装序列/长读段 vs 参考基因组 |
| BWA-MEM2 | 短读段比对 | Illumina 短读段 vs 参考基因组 |
| samtools | BAM/SAM 操作 | 排序、索引、统计 |
| bcftools | 变异检测 | SNP/InDel calling |
| MAFFT | 多序列比对 | 建树前的全局比对 |
| IQ-TREE | 最大似然系统发育 | 建进化树(支持 bootstrap) |
| FastTree | 快速近似建树 | 大规模序列(>1000 条) |
| ESMFold | 蛋白质结构预测 | AI 蛋白质折叠(用 A100 GPU) |
| BioPython | 通用生物信息学 | PDB 解析、序列操作、Entrez 查询 |
| 场景 | 正确工具 | 常见错误 |
|---|---|---|
| 组装基因组 vs 参考 | minimap2 | 用 BWA(BWA 是短读段工具) |
| 短读段 vs 参考 | BWA-MEM2 | 用 minimap2(不够精确) |
| 建进化树 | IQ-TREE (ML) | 用 NJ(邻接法太粗糙) |
| 蛋白质结构 | ESMFold 或 PDB 实验结构 | 盲目信任预测不看 pLDDT |
建议流程:
samtools / bcftools 做排序、索引和变异调用建议流程:
建议流程:
minimap2 的预设与输入输出格式samtools sort/view/index 的正确用法bcftools 变异调用链路iqtree 的 bootstrap 与模型参数blastn 的输出格式和阈值这些细节优先查 toolref。
import toytree
import matplotlib.pyplot as plt
tree = toytree.tree("tree.treefile")
canvas, axes, marks = tree.draw(
width=600, height=800,
tip_labels_align=True,
node_sizes=[0 if not n.is_leaf() else 8 for n in tree.treenode.traverse()],
)
# 按类群着色需自定义 node_colorsfrom pycirclize import Circos
circos = Circos(sectors={"genome": genome_length})
sector = circos.sectors[0]
# 轨道 1: 基因注释
track1 = sector.add_track((90, 95))
# 轨道 2: 变异密度
track2 = sector.add_track((80, 88))
# 轨道 3: GC 含量
track3 = sector.add_track((70, 78))
circos.savefig("circos.png", dpi=300)import py3Dmol
view = py3Dmol.view(width=800, height=600)
view.addModel(pdb_string, "pdb")
# 卡通表示 + 突变位点高亮
view.setStyle({"cartoon": {"color": "spectrum"}})
# 突变残基显示为球棍
view.addStyle({"resi": [484, 501, 681]},
{"stick": {"colorscheme": "redCarbon"}})
view.zoomTo()
view.show()import matplotlib.pyplot as plt
fig, ax = plt.subplots(figsize=(15, 4))
# x 轴: 蛋白位置
# y 轴: 携带该突变的变异株数量
# 颜色: 按功能域着色(NTD, RBD, S1/S2, S2)
ax.vlines(positions, 0, counts, colors=domain_colors, linewidth=1.5)
ax.scatter(positions, counts, c=domain_colors, s=30, zorder=5)
# 标注关键突变
for pos, name in key_mutations:
ax.annotate(name, (pos, counts[pos]), fontsize=8, rotation=45)| 序列长度 | VRAM 需求 | A100 40GB |
|---|---|---|
| < 400 aa | ~10 GB | 单 GPU |
| 400-800 aa | ~15-20 GB | 单 GPU |
| 800-1200 aa | ~25-35 GB | 单 GPU |
| > 1200 aa | > 40 GB | 需拆分域或多 GPU |
建议:预测蛋白质域(200-500 aa)而非全长(可能超出 VRAM)。
| 检查项 | 正确做法 | 常见错误 |
|---|---|---|
| 比对工具 | 组装用 minimap2,短读段用 BWA | 混用 |
| 建树方法 | ML (IQ-TREE) + bootstrap ≥1000 | 用 NJ 不做 bootstrap |
| 替换模型 | DNA: GTR+G4,蛋白: LG+G4 | 不做模型选择 |
| 结构预测 | 报告 pLDDT,与实验结构对比 | 盲目信任预测 |
| 突变命名 | 标准命名(N501Y 而非"501位天冬酰胺突变") | 非标准命名 |
| 趋同进化 | 区分趋同进化和共祖 | 混淆 |
| E-value | BLAST 结果按 e-value 过滤 | 不设阈值 |
minimap2 / BWA / BLAST© ZimoLiao, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Just SKILL.md in .claude/skills/bioinformatics of ZimoLiao/scholaraio.
Open the folder on GitHubat commit 777628b
Bioinformatics 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 |
|---|---|---|---|---|---|---|
| Bioinformatics this skillZimoLiao/scholaraio | 577 | — | ~1.4k | Automated safety check: Pass | MIT | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Clinvar Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.9k | Automated safety check: Notes | Apache-2.0 | |
| Metabolic Study Planneraiming-lab/AutoResearchClaw | 15k | — | ~1.9k | Automated safety check: Pass | MIT | |
| Dbsnp Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.4k | Automated safety check: Notes | Apache-2.0 |
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
K-Dense-AI/scientific-agent-skills
Estimates reaction fluxes inside cells from steady-state carbon-13 labeling data with a bundled mfapy-based solver, and reports which fluxes the data pin down.
google-deepmind/science-skills
A skill your agent uses when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls…
aiming-lab/AutoResearchClaw
Turns a broad metabolic modelling topic into a concrete, paper-shaped plan with organism, model, perturbations, metrics and figures before any FBA code is written.
google-deepmind/science-skills
A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.
aiming-lab/AutoResearchClaw
Runs a metabolic flux analysis from model loading to phenotype prediction and figures by handing work to four sub-agents in sequence.
ZimoLiao/scholaraio
A skill your agent uses when the user wants to create or inspect DOCX, PPTX, or XLSX files, generate a downloadable Office deliverable, or verify its structure and layout warnings with scholaraio…
ZimoLiao/scholaraio
A skill your agent uses when the user needs help choosing or organizing an academic-writing workflow by deliverable, stage, or format, including review articles, guided reading, paper sections, PPT…
ZimoLiao/scholaraio
A skill your agent uses when the user wants to browse arXiv preprints, search arXiv directly, fetch a PDF by arXiv ID or URL, or send a preprint into the ScholarAIO ingest pipeline.
ZimoLiao/scholaraio
A skill your agent uses when the user wants to verify citations in AI-generated or human-written text against the local knowledge base and catch hallucinated, wrong, or missing references.
ZimoLiao/scholaraio
A skill your agent uses when the user wants diagrams, flowcharts, architecture visuals, data relationships, timelines, concept maps, Mermaid, Graphviz, drawio, or polished paper figures generated…
ZimoLiao/scholaraio
A skill your agent uses when the user wants to survey a journal or field, fetch papers from OpenAlex, cluster topics, build exploration embeddings, or search named explore libraries under…
Categories
A skill your agent uses when working on bioinformatics workflows such as alignment, variant calling, phylogenetics, or protein-structure analysis, especially across BLAST, minimap2, samtools…. Bioinformatics is an agent skill from ZimoLiao/scholaraio. Use when working on bioinformatics workflows such as alignment, variant calling, phylogenetics, or protein-structure analysis, especially across BLAST, minimap2, samtools, bcftools, MAFFT, IQ-TREE, or ESMFold.
Bioinformatics fits situations like: working on bioinformatics workflows such as alignment; variant calling; protein-structure analysis; especially across BLAST.
Run `npx skills add ZimoLiao/scholaraio --skill bioinformatics -a claude-code`. Or copy the skill folder (.claude/skills/bioinformatics in ZimoLiao/scholaraio) into .claude/skills/bioinformatics in your project. Claude Code loads it when a task matches its description.
Run `npx skills add ZimoLiao/scholaraio --skill bioinformatics -a codex`. Or copy the skill folder (.claude/skills/bioinformatics in ZimoLiao/scholaraio) into .agents/skills/bioinformatics in your project. Codex loads it when a task matches its description.
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add ZimoLiao/scholaraio --skill bioinformatics -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bioinformatics, .gemini/skills/bioinformatics, .github/skills/bioinformatics and .opencode/skills/bioinformatics in your project.
Going by SKILL.md and its folder, Bioinformatics needs the command-line tools its instructions call (pip and conda). Our summary lists: Python 3.
SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
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.
Bioinformatics is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
About 1.4k tokens (SKILL.md is roughly 5.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
Skills that share tags, products or a category with Bioinformatics: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
ZimoLiao (a GitHub user) maintains it in ZimoLiao/scholaraio, which has 577 GitHub stars. The repository holds 43 skills in this directory. The repository was last updated on September 25, 2026.
Source: ZimoLiao/scholaraio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.