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 majiayu000/claude-skill-registry --skill fastq-quality-gptomics-bioskills --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.
# FASTQ Quality Scores 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 | |-------------|-------------------|----------| | 10 | 1 in 10 | 90% | | 20 | 1 in 100 | 99% | | 30 | 1 in 1000 | 99.9% | | 40 | 1 in 10000 | 99.99% | ## Code Patterns ### Calculate Average Quality per Read ```python for record in SeqIO.parse('reads.fastq', 'fastq'): quals = record.letter_annotations['phred_quality'] avg_qual = sum(quals) / len(quals) print(f'{record.id}: {avg_qual:.1f}') ``` ### Filter Reads by Mean Quality ```python def high_quality_reads(records, min_avg_qual=20): for record in records: quals = record.letter_annotations['phred_quality'] if sum(quals) / len(quals) >= min_avg_qual: yield record records = SeqIO.parse('reads.fastq', 'fastq') goo
- 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
- FASTQ Format Variants
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 majiayu000/claude-skill-registry --skill fastq-quality-gptomics-bioskills --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 majiayu000/claude-skill-registry, a repository with 534 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.