scATAC-seqAssessment of computational methods for the analysis of single-cell ATAC-seq data. ATAC-seq Data Standards and Prototype Processing Pipeline – ENCODE. ATAC-seq Data Standards and Prototype Processing Pipeline. The Assay for Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) experiment provides genome-wide profiles of chromatin accessibility. Briefly, the ATAC-seq method works as follows: loaded transposase inserts sequencing primers into open chromatin sites across the genome, and reads are then sequenced. The ends of the reads mark open chromatin sites. In its current form, the ATAC-seq pipeline is a prototype and will likely undergo substantial change within the next yearhttps://www.encodeproject.org/atac-seq/scATAC-seqbiotools:scATAC-seqhttp://edamontology.org/topic_3295Epigeneticshttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0204Gene regulationhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/operation_3891Essential dynamicshttp://edamontology.org/operation_3222Peak callinghttp://edamontology.org/operation_3432Clusteringhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3192Sequence trimming10.1186/S13059-019-1854-531739806PMC6859644Luca Pinellolpinello@mgh.harvard.eduhttps://orcid.org/0000-0003-1109-3823Person