A copy-number variation detection pipeline for single cell sequencing data on BGI online

The revolutionary invention of single-cell sequencing technology carves out a new way to delineate intra tumor heterogeneity and traces the evolution of single cells at the molecular level. To cater for fast and convenient needs in calling copy-number variations in analyzing single-cell sequencing data, a systematical protocol and a working pipeline is reported. The proposed pipeline consists of six modules in total. Every module in the pipeline is designed to achieve unitary task, and is unattached, thus facilitating user-customized applications. Our proposed pipeline is implemented on BGI Online to provide a user-friendly graphical interface for processing single-cell sequencing data. It consists of automatic and powerful functionalities that would facilitate the management of online Web modules for a full range of analysis, such as read alignment, genome bias correction, bin segmentation, copy number variants (CNVs) calling, data clustering, and visualization. The pipeline is open for public usage and its address is http://www.bgionline.cn.