PEPATAC

PEPATAC processes ATAC-seq data to perform adapter trimming, read alignment (including serial alignment to the mitochondrial genome), peak calling, and generation of QC metrics and tracks to support chromatin accessibility analysis.

Key Features:

• Optimization for Speed and Accuracy: Leverages ATAC-seq-specific characteristics to enhance processing speed and accuracy via adapter trimming, read mapping, peak calling, and generation of bigwig tracks and transcription start site (TSS) enrichment files.
• Comprehensive Output Generation: Produces quality control plots, summary statistics, bigwig tracks, TSS enrichment files, and data in widely used formats for downstream analyses.
• Modular Design and Standardization: Provides a modular architecture with components usable independently and employs standard definition formats and metadata APIs available in R and Python.
• Fault Tolerance and Restartability: Implements fault-tolerant, restartable execution to ensure reliable processing across computational environments.
• Serial Alignment to Mitochondrial Genome: Performs serial alignment to the mitochondrial genome to improve the accuracy of alignment statistics and quality control metrics.
• Integration with Portable Encapsulated Projects (PEPs): Supports integration with PEPs to decouple and make sample metadata reusable across analyses.

Scientific Applications:

• ATAC-seq preprocessing and QC: Prepares ATAC-seq datasets by producing trimmed and aligned reads, peaks, and QC metrics for chromatin accessibility analysis.
• Large-scale genomic and project-based studies: Provides standardized outputs and metadata integration to support organization and analysis of large-scale biological research projects.

Methodology:

Performs adapter trimming, read mapping including serial mitochondrial alignment, peak calling, generation of bigwig tracks and TSS enrichment files, produces quality control plots and summary statistics, and integrates sample metadata via Portable Encapsulated Projects (PEPs) and metadata APIs for R and Python.