Dr.seq: a quality control and analysis pipeline for droplet sequencing
Dr.seq: a quality control and analysis pipeline for droplet sequencing
复制标题
Dr.seq：液滴测序的质量控制和分析流程
DOI：
10.1093/bioinformatics/btw174
复制
发表时间：
2016
期刊：
影响因子：
5.8
通讯作者：
Yong Zhang
中科院分区：
文献类型：
--
作者：
Xiao Huo;Sheng'en Hu;Chengchen Zhao;Yong Zhang
动机
Drop-seq最近成为一种强大的技术，可以同时分析数千个单个细胞的基因表达。目前，Drop-seq技术需要改进，质量控制（QC）步骤对于此类数据分析至关重要。迫切需要一种方便而全面的方法来获得专用的QC并确定超高维数据集的单元之间的关系。
结果
我们开发了Dr.seq，一个用于Drop-seq数据的QC和分析管道。通过应用此管道，Dr.seq为给定的Drop-seq数据提供四组QC测量，包括读段水平、批量细胞水平、单个细胞水平和细胞聚类水平QC。我们在模拟和发表的Drop-seq数据上评估了Dr.seq。这两项评估都显示出可靠的结果。总的来说，Dr.seq是一个全面的QC和分析管道，专为Drop-seq数据设计，可以轻松扩展到其他基于小滴的数据类型。
可用性和执行
Seq博士可在以下网址免费获得：http：//www.tongji.edu.cn/zhanglab/drseq和https://bitbucket.org/tarela/drseq
接触
yzhang@tongji.edu.cn
补充资料
补充数据可在Bioinformatics在线获得。
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.