title: Dr.seq: a quality control and analysis pipeline for droplet sequencing.
abstract: 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.
  
  
  
  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.
  
  
  
  Dr.seq is freely available at: http://www.tongji.edu.cn/∼zhanglab/drseq and https://bitbucket.org/tarela/drseq
  
  
  
  yzhang@tongji.edu.cn
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 20092, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Huo
authors.affiliation: School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 20092, China.
authors.forename: Sheng'en
authors.initials: S
authors.lastname: Hu
authors.affiliation: School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 20092, China.
authors.forename: Chengchen
authors.initials: C
authors.lastname: Zhao
authors.affiliation: School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 20092, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D016000:Cluster Analysis; D059014:High-Throughput Nucleotide Sequencing; D011786:Quality Control; D012984:Software