SnapATAC2: A Python/Rust package for single-cell epigenomics analysis

SnapATAC2 is the successor of the SnapATAC R package, featuring:

• Faster and less memory usage than the R version and other alternatives, scale to >1M cells.

• Blazingly fast preprocessing tools for BAM to fragment files conversion and count matrix generation.

• One of the best dimension reduction algorithms for single-cell ATAC data.

• End-to-end analysis pipeline, including preprocessing, dimension reduction, clustering, data integration, peak calling, differential analysis, motif analysis, regulatory network analysis.

• Seamless integration with other single-cell analysis packages such as scanpy.

• Implementation of fully backed AnnData.

How to cite

The SnapATAC2 manuscript has not been published yet. The key algorithms used in SnapATAC2 have been described in the following papers:

• Zhang, K. et al. A single-cell atlas of chromatin accessibility in the human genome. Cell 184, 5985-6001.e19 (2021).

• Fang, R. et al. Comprehensive analysis of single cell ATAC-seq data with SnapATAC. Nat Commun 12, 1337 (2021).