About
A bioinformatics analysis pipeline for ATAC-seq data built using Nextflow DSL2, providing comprehensive chromatin accessibility analysis from raw reads to differential accessibility results. Features multiple aligners (BWA, Bowtie2, STAR, Chromap), peak calling with MACS2, differential analysis with DESeq2, and automated QC reporting with MultiQC and ataqv.
Tech Stack
NextflowPythonRDockerSingularityConda
Research Paper
DOI: 10.5281/zenodo.2634132Quick Start
nextflow run nf-core/atacseq --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 --read_length <50|100|150|200> -profile docker