bio-fastq-quality
Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-fastq-quality --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # FASTQ Quality Scores **"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. ## Required Imports ```python from Bio import SeqIO from Bio.Seq import Seq ``` ## Accessing Quality Scores Quality scores are stored in `letter_annotations['phred_quality']` as a list of integers. ```python for record in SeqIO.parse('reads.fastq', 'fastq'): qualities = record.letter_annotations['phred_quality'] print(record.id, qualities[:10]) # First 10 quality scores ``` ## Quality Score Basics | Phred Score | Error Probability | Accuracy | |-------------|--------------
- Version Compatibility
- Required Imports
- Accessing Quality Scores
- Quality Score Basics
- Code Patterns
- Calculate Average Quality per Read
- Filter Reads by Mean Quality
- Filter by Minimum Quality at Any Position
- Trim Low-Quality Ends (3' Trimming)
- Sliding Window Quality Trim
- Quality Statistics Summary
- Per-Position Quality Profile
- Count Reads by Quality Threshold
- Remove N Bases and Low Quality Together
What does the bio-fastq-quality skill do?
Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-fastq-quality --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.