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

bio-read-qc-quality-reports

Maintainer FreedomIntelligence · Last updated April 1, 2026

Generate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter content, GC bias, duplication levels, and overrepresented sequences. Use when performing initial QC on raw sequencing data or validating preprocessing results.

OpenClawNanoClawAnalysisReproductionbio-read-qc-quality-reports🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcgenerate

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: fastqc *.fastq.gz then multiqc.
Generate quality reports for FASTQ files using FastQC and aggregate multiple reports with MultiQC.
Run quality control on FASTQ files" → Generate per-base quality, adapter content, and duplication plots, then aggregate across samples. CLI: fastqc *.fastq.gz then multiqc.
fastqc -o qc_reports/ sample_R1.fastq.gz sample_R2.fastq.gz.

Source Doc

Excerpt From SKILL.md

Output Files

FastQC produces two files per input:

sample_fastqc.html - Interactive HTML report
sample_fastqc.zip - Data files and images

Key Modules

Module	What It Shows	Warning Signs
Per base sequence quality	Quality scores across read	Drop below Q20 at 3' end
Per sequence quality	Quality score distribution	Bimodal distribution
Per base sequence content	Nucleotide composition	Imbalance at start (normal)
Per sequence GC content	GC distribution	Secondary peak (contamination)
Per base N content	Unknown bases	High N content
Sequence length distribution	Read lengths	Unexpected variation
Sequence duplication	Duplicate reads	High duplication (PCR)
Overrepresented sequences	Common sequences	Adapter contamination
Adapter content	Adapter sequences	Visible adapter curves