BICF ATAC-seq Pipeline

Introduction

BICF ATAC-seq is a bioinformatics best-practice analysis pipeline used for ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) data analysis at BICF at UT Southwestern Dept. of Bioinformatics.

The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.

This pipeline is primarily used with a SLURM cluster on the BioHPC Cluster. However, the pipeline should be able to run on any system that Nextflow supports.

Additionally, the pipeline is designed to work with Astrocyte Workflow System using a simple web interface.