I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples

Area of Science:

• Genomics
• Epigenetics
• Bioinformatics

Background:

• Assay for Transposase Accessible Chromatin (ATAC-seq) enables open chromatin profiling, crucial for understanding cellular transcriptional programs.
• The increasing volume of clinical ATAC-seq data necessitates efficient analysis tools for deriving clinical insights.
• Current limitations in user-friendly software hinder non-computational scientists from analyzing their own ATAC-seq data.

Purpose of the Study:

• To develop an accessible, user-friendly software application for the pre-processing and management of ATAC-seq samples.
• To empower non-computational scientists with the ability to analyze their own ATAC-seq datasets.
• To facilitate the systematic analysis of clinical epigenomic data.

Main Methods:

• Developed interactive-ATAC (I-ATAC), a cross-platform desktop application with a graphical user interface.
• Integrated established command-line tools (FASTQC, Trimmomatic, BWA, Picard, ATAC_BAM_shiftrt_gappedAlign.pl, Bedtools, Macs2) into automated, parallelized pipelines.
• Tested I-ATAC performance on public ATAC-seq datasets (GM12878, CD4+T cells) and compared its features with existing LIMS.

Main Results:

• I-ATAC successfully integrates multiple bioinformatics tools into an intuitive platform for ATAC-seq data pre-processing.
• The application automates complex data analysis pipelines, making them accessible to users without extensive computational expertise.
• Performance testing confirmed the efficacy of I-ATAC in handling ATAC-seq datasets.

Conclusions:

• I-ATAC democratizes ATAC-seq data analysis, enabling broader scientific participation in epigenomic research.
• The software facilitates the extraction of clinical insights from large-scale epigenomic datasets.
• I-ATAC's versatility extends to Whole Genome Sequencing (WGS) and Chromatin Immunoprecipitation sequencing (ChIP-seq) data analysis.