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

bio-workflows-fastq-to-variants

Maintainer FreedomIntelligence · Last updated April 1, 2026

Complete FASTQ → alignment → variant calling pipeline.

OpenClawNanoClawAnalysisReproductionbio-workflows-fastq-to-variants🧠 bioos extended suitebioos extended bioinformatics suitecomplete

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Complete pipeline from raw DNA sequencing FASTQ files to filtered variant calls.
fastp -i sample_R1.fastq.gz -I sample_R2.fastq.gz \ -o sample_R1.trimmed.fq.gz -O sample_R2.trimmed.fq.gz \ --detect_adapter_for_pe \ --qualified_quality_phred 20 \ --length_required 50 \ --html sample_fastp.html.

Source Doc

Excerpt From SKILL.md

Batch processing

for sample in sample1 sample2 sample3; do fastp -i ${sample}_R1.fastq.gz -I ${sample}_R2.fastq.gz
-o trimmed/${sample}_R1.fq.gz -O trimmed/${sample}_R2.fq.gz
--detect_adapter_for_pe
--html qc/${sample}_fastp.html done


**QC Checkpoint 1:** Check fastp reports
- Q30 bases >85% (DNA typically higher quality than RNA)
- Adapter content <1%
- No unusual GC distribution

## Index reference (once)

bwa-mem2 index reference.fa

## Align with read group info

for sample in sample1 sample2 sample3; do
    bwa-mem2 mem -t 8 \
        -R "@RG\tID:${sample}\tSM:${sample}\tPL:ILLUMINA\tLB:lib1" \
        reference.fa \
        trimmed/${sample}_R1.fq.gz \
        trimmed/${sample}_R2.fq.gz \
    | samtools view -bS - > aligned/${sample}.bam
done
bash
samtools flagstat aligned/${sample}.bam

Mapped reads >95%
Properly paired >90%

Use cases

Use bio-workflows-fastq-to-variants for genomics and bioinformatics workflows.
Apply bio-workflows-fastq-to-variants to sequencing, variant, or omics analysis tasks.