Dr.seq: A quality control and analysis pipeline for droplet sequencing

Abstract

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 datasets. 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. Availability and Implementation: Dr.seq is freely available at: http://www.tongji.edu.cn/∼zhanglab/drseq and https://bitbucket.org/tarela/drseq Contact: Supplementary information: Supplementary data are available at Bioinformatics online.