CPLSTool: A Framework to Generate Automatic Bioinformatics Pipelines

Abstract

Many bioinformatics tools have been developed for data analysis and focus on some specific problems. However, one program is not enough to complete the data mining. We developed CPLSTool (https://github.com/maoshanchen/CPLSTool) that can compress multiple bioinformatics tools and the produced pipeline can be used for data anlaysis repeatly. The most significant advantage of using CPLSTool is to save waiting time, compared to step-by-step analysis. In addition, some steps for the data analysis can be run parallely in order to save the program running time. We used CPLSTool to build an automatic pipeline based on QIIME and analyzed skin 16S rRNA data. The results showed that a total of 102 minutes can be saved using CPLSTool and the visualization of results improves our understanding of the results. CPLSTool can be applied in any kind of data analysis, including genomic, transcriptomic, proteomic and metagenomic data analysis. The use of CPLSTool will improve our understanding of data analysis and save time and computing resources.