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SKILL verified MIT Self-run

Bio Read Qc Trimming

skill-onescience-ai-oneskills-read-qc-trimming · by onescience-ai

FASTQ 质控与剪切 skill。用于 raw FASTQ 的 FastQC/fastp/MultiQC、adapter 去除、质量过滤、长度过滤、UMI 预处理、paired-end 一致性检查和下游比对/定量前数据准备。

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Install

$ agentstack add skill-onescience-ai-oneskills-read-qc-trimming

✓ scanned · ✓ verified, works with Claude Code, Cursor, and more.

Security review

✓ Passed

No issues found. Passed automated security review. · v0.1.0 How review works →

  • ✓ Prompt-injection patterns
  • ✓ Secret / credential exfiltration
  • ✓ Dangerous shell & filesystem operations
  • ✓ Untrusted network calls
  • ✓ Known-malicious package signatures

What it can access

  • ✓ Network access No
  • ✓ Filesystem access No
  • ✓ Shell / process execution No
  • ✓ Environment & secrets No
  • ✓ Dynamic code execution No

From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.

View the full security report →

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Reliability & compatibility

✓ Security review passed
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Declared compatibility

Claude CodeClaude Desktop

Compatibility is declared by the source manifest. End-to-end runtime verification is coming, see below.

Preview Execution monitoring

We're building live execution health for every listing: tool-call success rate, median latency, uptime, and last-checked timestamps, measured, not self-reported. It isn't live yet, so we don't show numbers we can't stand behind.

How agent discovery & health will work →
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About

FASTQ 质控与剪切

推荐流程

  1. 明确 single-end/paired-end、read length、文库类型、UMI、barcode、平台。
  2. 做原始 QC：per-base quality、adapter、duplication、GC、overrepresented sequences。
  3. 执行 trimming/filtering：adapter detection、Q threshold、minimum length、polyG/polyX、UMI handling。
  4. 做剪切后 QC，并汇总为 MultiQC。
  5. 输出 trimmed FASTQ、QC HTML/JSON、过滤统计和下游建议。

QC 检查点

  • Q30 比例和低质量尾部。
  • adapter 是否充分去除。
  • paired-end 文件是否同步。
  • 过滤后 read 数是否异常下降。

交接物

bio_task_family: read-qc
input_fastq:
library_type:
paired_end:
umi_or_barcode:
trim_strategy:
qc_reports:
downstream_workflow:
execution_entry:

禁止事项

  • 不要在不了解 UMI/barcode 结构时随意剪切 read 头部。
  • 不要只看剪切后指标，必须保留剪切前后对比。

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

Install and usage instructions live in the source repository linked above.

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Versions

  • v0.1.0 Imported from the upstream source.

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