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bio-workflows-atacseq-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

ATAC-seq: trimming → alignment → peak calling → differential.

OpenClawNanoClawAnalysisReproductionbio-workflows-atacseq-pipeline🧠 bioos extended suitebioos extended bioinformatics suiteatac

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-workflows-atacseq-pipeline

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Complete workflow from raw ATAC-seq FASTQ files to accessibility peaks, differential analysis, and TF footprinting.
NEXTERA_R1="CTGTCTCTTATACACATCT" NEXTERA_R2="CTGTCTCTTATACACATCT.
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 \ --adapter_sequence ${NEXTERA_R1} \ --adapter_sequence_r2 ${NEXTERA_R2} \ --qualified_quality_phred 20 \ --length_required 25 \ --html qc/${sample}_fastp.html done.

Source Doc

Excerpt From SKILL.md

Build index (once)

bowtie2-build genome.fa bt2_index/genome

Align with ATAC-seq specific settings

for sample in sample1 sample2 sample3; do bowtie2 -p 8 -x bt2_index/genome
-1 trimmed/${sample}_R1.fq.gz
-2 trimmed/${sample}_R2.fq.gz
--very-sensitive
--no-mixed --no-discordant
-X 2000
2> aligned/${sample}.log |
samtools view -@ 4 -bS -q 30 -f 2 - |
samtools sort -@ 4 -o aligned/${sample}.bam done


## Step 3: BAM Processing

ATAC-seq requires special processing: removing mitochondrial reads, shifting reads for Tn5 insertion, and removing duplicates.

Alternative manual Tn5 shift with bedtools:
```bash

Use cases

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