数据与复现生物信息与基因组学FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-read-qc-quality-filtering

维护者 FreedomIntelligence · 最近更新 2026年4月1日

Filter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, remove low-quality bases from read ends, and discard reads below thresholds. Use when reads have poor quality tails or require minimum quality for downstream analysis.

OpenClawNanoClaw分析处理复现实验bio-read-qc-quality-filtering🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcfilter

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-qc-quality-filtering

维护者: FreedomIntelligence
许可: MIT
最近更新: 2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

CLI：trimmomatic PE ，支持 SLIDINGWINDOW 、 MINLEN options。
CLI：fastp --qualified_quality_phred 20 --length_required 50。
Trim low-quality bases 、 filter reads ，使用 Trimmomatic sliding window 或 fastp quality filtering。
Filter reads by quality" → Remove low-quality bases 、 discard reads below quality/length thresholds. CLI：trimmomatic PE ，支持 SLIDINGWINDOW 、 MINLEN options CLI：fastp --qualified_quality_phred 20 --length_required 50。
trimmomatic SE input.fq output.fq \ SLIDINGWINDOW：4：20 MINLEN：36。

原始文档

SKILL.md 摘录

Trimmomatic Operations

Operation	Syntax	Description
LEADING	LEADING:Q	Remove leading bases below quality Q
TRAILING	TRAILING:Q	Remove trailing bases below quality Q
SLIDINGWINDOW	SLIDINGWINDOW:W:Q	Cut when W-bp window average < Q
MINLEN	MINLEN:L	Discard reads shorter than L
CROP	CROP:L	Cut read to max length L
HEADCROP	HEADCROP:N	Remove first N bases
AVGQUAL	AVGQUAL:Q	Drop read if average quality < Q
MAXINFO	MAXINFO:L:S	Balance length and quality
TOPHRED33	TOPHRED33	Convert to Phred33 encoding
TOPHRED64	TOPHRED64	Convert to Phred64 encoding

Aggressive 3' trimming

trimmomatic SE input.fq output.fq
TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36

Trim both ends, strict filtering

trimmomatic SE input.fq output.fq
LEADING:10 TRAILING:10 SLIDINGWINDOW:4:25 MINLEN:50

适用场景

适合在reads have poor quality tails 或 require minimum quality ，用于 downstream analysis时使用。

不适用场景

Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。

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adapter-trimming - Remove adapters before quality filtering
quality-reports - Check quality before/after filtering
fastp-workflow - All-in-one preprocessing

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