Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-fastq-quality

Maintainer FreedomIntelligence · Last updated April 1, 2026

Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.

OpenClawNanoClawAnalysisReproductionbio-fastq-quality🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcwork

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Python: SeqIO.parse() with letter_annotations['phred_quality'] (BioPython).
Filter my FASTQ reads by quality score" → Access, analyze, and filter Phred quality scores, trim low-quality bases, and generate per-position quality profiles. Python: SeqIO.parse() with letter_annotations['phred_quality'] (BioPython).
Analyze and manipulate FASTQ quality scores using Biopython.
solexa_score = 10 phred_score = phred_quality_from_solexa(solexa_score).

Source Doc

Excerpt From SKILL.md

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+):

Use cases

Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

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