SIP: An Interchangeable Pipeline for scRNA-seq Data Processing

Multiple steps of bioinformatics processing are needed to convert the raw scRNA-seq data to information that can be used in downstream analyses and in building cell atlases. Dozens of software packages have been developed and different labs tend to have different preferences on choices of the workflow. Such diversity can cause difficulties in future efforts of aggregating data from multiple labs, and also difficulties for new labs to start in this field. A few pipelines have been developed to help integrating multiple steps into a whole, but the fixed software architecture makes it hard for developers to add new features or exchange parts in the pipeline. We presented SIP, a Single-cell Interchangeable Pipeline. It is a one-stop platform for the processing of scRNA-seq data from multiple platforms, and will also support for other types of data like scATAC-seq data. SIP utilizes container technology to solve the deployment dilemma when handling multiple packages and provides an easy-to-use interface for users to conduct the complicated multi-step process from raw data to final results with a single command. It also allows advanced users to assemble different versions of the pipeline by interchanging parts or adding new modules. SIP is available at https://github.com/XuegongLab/SIP under the GPL-3.0 license.