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Dr.seq: a quality control and analysis pipeline for droplet sequencing
Xiao Huo1, Sheng'en Hu1, Chengchen Zhao1
1School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 20092, China.
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:
yzhang@tongji.edu.cn
Supplementary Information:
Supplementary data are available at Bioinformatics online.
