Alevin-fry-atac

Alevin-fry-atac enables rapid and memory-frugal mapping of single-cell ATAC-seq data utilizing virtual colors for accurate genomic pseudoalignment.

Key Features:

• Virtual color pseudoalignment: Partitions each reference into overlapping bins of fixed maximal extent on the reference sequences that are treated as distinct "colors" from the perspective of the pseudoalignment algorithm.
• High scalability: When using 32 threads, achieves 2.8 times faster mapping than Chromap while using only 33% of Chromap's memory.
• Unified single-cell processing ecosystem: Brings single-cell ATAC-seq processing together with single-cell RNA-seq processing via alevin-fry.

Scientific Applications:

• Single-cell ATAC-seq data mapping: Processes and maps single-cell ATAC-seq reads directly to the genome as an alternative to alignment-based methods.
• Peak and cluster generation: Produces peaks and clusters that show high concordance with those obtained from Chromap and the Cell Ranger ATAC pipeline.

Methodology:

Alevin-fry-atac applies a modified pseudoalignment procedure that partitions each reference into "virtual colors"—overlapping bins of fixed maximal extent on the reference sequences treated as distinct colors from the perspective of the pseudoalignment algorithm—to process and map single-cell ATAC-seq data.