scATACpipe is a bioinformatic pipeline (powered by Nextflow) for single-cell ATAC-seq (scATAC-seq) data analysis. scATACpipe enables users to perform the end-to-end analysis of scATAC-seq data with three sub-workflow options for preprocessing that leverage 10x Genomics Cell Ranger ATAC software, the ultra-fast Chromap procedures, and a set of custom scripts implementing current best practices for scATAC-seq data preprocessing. The pipeline extends the R package ArchR for downstream analysis with added support to any eukaryotic species with an annotated reference genome.
Hu K, Liu H, Lawson ND, Zhu LJ. scATACpipe: A nextflow pipeline for comprehensive and reproducible analyses of single cell ATAC-seq data. Front Cell Dev Biol. 2022 Sep 27;10:981859. doi: 10.3389/fcell.2022.981859. PMID: 36238687; PMCID: PMC9551270.