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scholaraio: Skill for Claude Code

.claude/skills/bioinformatics/SKILL.md

bioinformatics is a skill for Claude Code from ZimoLiao/scholaraio. It costs 55 tokens per session (2,596 once invoked), scanned A, original, MIT.

A guide to bioinformatics, the use of computer tools to analyse biological data such as DNA, RNA, and proteins. It routes tasks to tools for sequence searches, alignment, variant detection, evolutionary trees, and protein-structure prediction.

In plain words
What is it for?
Use it for BLAST similarity searches, sequence alignment, processing sequencing files, finding genetic variants, comparing multiple sequences, building phylogenetic trees, and predicting protein structures.
Why use it?
It prevents treating many different programs as one system or choosing a tool without first identifying the data and task. It also helps maintain a sensible analysis workflow when one tool's documentation is incomplete.

Skill for Claude Code

Written for Claude Code: installed under .claude/.

This is ZimoLiao/scholaraio's own configuration. It tells Claude Code how to work on scholaraio itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything scholaraio configures →

Part of the scholaraio plugin — 44 skills, 1 hook shipped together

not rated 584repo +1 10d ago A scan SkillSpector: pass 55 tokens original MIT
View source ↗ ZimoLiao/scholaraio zimoliao.github.io
Reuse

Borrowing it

Nothing to install: this file belongs to ZimoLiao/scholaraio. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/ZimoLiao/scholaraio/main/.claude/skills/bioinformatics/SKILL.md
Clone the repo
git clone --depth 1 https://github.com/ZimoLiao/scholaraio

Made for: Claude Code.

Or install scholaraio, the plugin that ships this one along with the rest of its 44 skills, 1 hook.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for bioinformatics

README.md
[![agentmods](https://agentmods.dev/badge/skills/zimoliao/scholaraio/bioinformatics/github.svg)](https://agentmods.dev/skills/zimoliao/scholaraio/bioinformatics)
Your own site
<a href="https://agentmods.dev/skills/zimoliao/scholaraio/bioinformatics"><img src="https://agentmods.dev/badge/skills/zimoliao/scholaraio/bioinformatics/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for bioinformatics

Your own site · 80×15
<a href="https://agentmods.dev/skills/zimoliao/scholaraio/bioinformatics"><img src="https://agentmods.dev/badge/skills/zimoliao/scholaraio/bioinformatics.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 55 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,596 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector pass 7 Sept 2026
How audits are shown
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00055 $0.02596
Opus 5.5 $0.00022 $0.01038
Sonnet 5.5 $0.00011 $0.00519
Haiku 4.5 $0.00006 $0.00260

Measured 2mo ago against content hash fd0ad30530bb, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

bioinformatics scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.claude/skills/bioinformatics/SKILL.md · 250 lines

How it starts

The opening of the file, as written. The whole thing — 250 lines — stays where its author put it; the contents beside it link to each section on GitHub.

生物信息学分析

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：

  • 它负责告诉 agent 哪类问题该用哪类工具、标准分析链路是什么、哪些生信规范不能忽略
  • 它不承担各个命令行工具的完整手册职责
  • 具体 CLI 选项、子命令、输入输出细节统一去查 scholaraio toolref

Agent 默认协议（toolref-first, toolchain-aware）

Bioinformatics 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：

  1. 先判断当前任务属于哪类：
    • 同源搜索：BLAST
    • 组装序列比对：minimap2
    • BAM/SAM 处理：samtools
    • 变异调用：bcftools
    • 多序列比对：MAFFT
    • 建树：IQ-TREE
    • 结构预测：ESMFold
  2. 再用 toolref show bioinformatics <program> ... 或 search --program <program> 查对应程序
  3. 不要把“生信工具链”当一个大黑箱查
  4. 如果某个子工具当前 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
  5. 不要让普通用户自己补齐某个子工具的 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
  • 当前覆盖不全时，复杂度应由 agent 吸收，而不是由用户承担

前置条件

# 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。

何时使用

适合：

  • 序列相似性搜索、参考比对、变异检测、系统发育树构建
  • 蛋白质结构预测与突变位点解释

不适合：

  • 没有明确数据类型就盲选工具
  • 把生信流程当“黑箱一键按钮”，不检查质量控制和统计假设

Toolref 优先

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：

  • 在决定工具前先确认数据类型：组装序列、短读段、蛋白序列、树推断
  • 写命令前先查对应手册页，而不是靠记忆拼接参数
  • 报告结果时带上阈值、模型和置信度，而不是只给一张图

如果遇到覆盖缺口：

  • 先回退到对应子工具的官方手册
  • 在回答里明确指出是哪个子工具存在 toolref 覆盖不足
  • 不要让用户为了当前分析去维护 toolref

核心工具链

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

Read the full file on GitHub · 250 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 2mo ago First seen · 250 lines · 55 tokens per session scan A fd0ad30530bb

Subscribe to this mod's changes

bioinformatics is a skill published in the GitHub repository ZimoLiao/scholaraio (584 stars, last pushed 10d ago), licensed MIT. It adds 55 tokens to every session and 2,596 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Scientificagentic-scienceagentic-searchai-agentcomputational-researchresearch-workflowscientific-computing
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template-reproducibility-auditdocxology/templateSkill23yesterdayApache-2.0A70Claude Code, Codex