Motivation: Drop-seq has recently emerged as a powerful technology to analyze gene expression from thousands of individual cells simultaneously.Currently,Drop-seq technology requires refinement,and quality control (QC) steps are critical for such data analysis.There is a strong need for a convenient and comprehensive approach to obtain dedicated QC and to determine the relationships between cells for ultra-high-dimensional data sets.Results: We developed Dr.seq,a QC and analysis pipeline for Drop-seq data.By applying this pipeline,Dr.seq provides four groups of QC measurements for given Drop-seq data,including reads level,bulk-cell level,individual-cell level and cell-clustering level QC.We assessed Dr.seq on simulated and published Drop-seq data.Both assessments exhibit reliable results.Overall,Dr.seq is a comprehensive QC and analysis pipeline designed for Drop-seq data that is easily extended to other droplet-based data types.