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数据与复现
BI
bio-fastq-quality
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-fastq-quality
- 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
核心说明
- Python：SeqIO.parse() ，支持 letter_annotations['phred_quality'] (BioPython)。
- Filter my FASTQ reads by quality score" → Access，analyze，、 filter Phred quality scores，trim low-quality bases，、 generate per-position quality profiles. Python：SeqIO.parse() ，支持 letter_annotations['phred_quality'] (BioPython)。
- 分析 、 manipulate FASTQ quality scores ，使用 Biopython。
- solexa_score = 10 phred_score = phred_quality_from_solexa(solexa_score)。
原始文档
SKILL.md 摘录
Accessing Quality Scores
Quality scores are stored in letter_annotations['phred_quality'] as a list of integers.
Quality Score Basics
| Phred Score | Error Probability | Accuracy |
|---|---|---|
| 10 | 1 in 10 | 90% |
| 20 | 1 in 100 | 99% |
| 30 | 1 in 1000 | 99.9% |
| 40 | 1 in 10000 | 99.99% |
Sliding Window Quality Trim
Goal: Trim a read at the first position where average quality in a sliding window drops below threshold.
Approach: Slide a fixed-size window across quality scores; when the window average falls below the cutoff, truncate the record at that position.
Reference (BioPython 1.83+):
适用场景
- 适合在analyzing read quality，filtering by quality，trimming low-quality bases，或 generating quality reports时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- read-sequences - Parse FASTQ files
- filter-sequences - Filter reads by other criteria (length, content)
- paired-end-fastq - Handle R1/R2 paired quality filtering
- sequence-statistics - Generate summary statistics including quality
- alignment-files - After filtering, align reads with bwa/bowtie2; quality scores in BAM
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