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Research ArticleOpen Access

CPLSTool: A Framework to Generate Automatic Bioinformatics Pipelines

Volume 11 - Issue 5

Sifen Lu1, Jing Song2 and Maoshan Chen*3

  • Author Information Open or Close
    • 1Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital of Sichuan University, No. 37, Wuhou District National School Lane, Chengdu, Sichuan, China
    • 2Department of Rheumatology and Immunology, Changzheng Hospital, Naval Medical University, 415 Fengyang Road, Shanghai, China
    • 3Department of Clinical Heamatology, Australia
    • *Corresponding author: Maoshan Chen, Australian Centre for Blood Diseases, Department of Clinical Heamatology, Central Clinical School, Melbourne, Victoria, Australia

Received: November 26, 2018;   Published: December 11, 2018

DOI: 10.26717/BJSTR.2018.11.002172

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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.

Keywords :Bioinformatics; Pipelines; Next-Generation Sequencing; Data Analysis

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