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PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments.

Jason P Smith1, M Ryan Corces2, Jin Xu2

  • 1Center for Public Health Genomics, University of Virginia, VA,22908, USA.

NAR Genomics and Bioinformatics
|December 3, 2021
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Summary

PEPATAC is a new analysis pipeline for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data. It offers speed, accuracy, and flexibility for projects of all sizes, simplifying downstream analysis and improving quality control metrics.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Chromatin accessibility data from ATAC-seq is expanding rapidly.
  • Standardized analysis pipelines are crucial for managing and interpreting this data.
  • Existing pipelines may lack the flexibility or specific features needed for diverse ATAC-seq projects.

Purpose of the Study:

  • To introduce PEPATAC, a novel, standardized analysis pipeline for ATAC-seq data.
  • To provide a robust and portable solution for ATAC-seq projects of varying scales.
  • To enhance the speed, accuracy, and analytical capabilities of ATAC-seq data processing.

Main Methods:

  • Development of a modular and restartable ATAC-seq analysis pipeline.
  • Leveraging unique features of ATAC-seq data for optimized performance.
  • Incorporation of serial alignment to the mitochondrial genome for improved QC metrics.
  • Implementation of metadata APIs in R and Python for simplified downstream analysis.

Main Results:

  • PEPATAC provides optimized speed and accuracy for ATAC-seq data analysis.
  • The pipeline generates convenient quality control plots and summary statistics.
  • It supports various data formats and offers simplified downstream analysis through standardized formats and modularity.
  • Serial alignment to the mitochondrial genome enhances alignment statistics and QC.

Conclusions:

  • PEPATAC is a robust, portable, and user-friendly first step for any ATAC-seq project.
  • The pipeline facilitates efficient and accurate analysis of ATAC-seq data, from small to large-scale projects.
  • Its features simplify data interpretation and downstream analyses, making it a valuable tool for researchers.