The prototype ATAC-seq pipeline was developed by Anshul Kundaje's lab at Stanford University. Upon revision and full implementation, it will be a part of the ENCODE Uniform Processing Pipelines series. The full ATAC-seq pipeline code is available on Github. The ENCODE ATAC-seq pipeline is used for quality control and statistical signal processing of short-read sequencing data, producing alignments and measures of enrichment. The pipeline shown here assumes the following defaults: align_only is false, pipeline_type is 'atac', all fastq and adapter files are defined in a single files, true_rep_only is false, disable_xcor is false, disable_ataqc is false, enable_idr is true (false is the default value, but set to true so all the possible steps are shown).