QuaPra: Efficient transcript assembly and quantification using quadratic programming with Apriori algorithm

Abstract

RNA sequencing (RNA-seq) has greatly facilitated the exploring of transcriptome landscape for diverse organisms. However, transcriptome reconstruction is still challenging due to various limitations of current tools and sequencing technologies. Here, we introduce an efficient tool, QuaPra (Quadratic Programming combined with Apriori), for accurate transcriptome assembly and quantification. QuaPra could detect at least 26.5% more low abundance (0.1–1 FPKM) transcripts with over 2.1% increase of sensitivity and precision on simulated data compared to other currently popular tools. Moreover, around one-quarter more known transcripts were correctly assembled by QuaPra than other assemblers on real sequencing data. QuaPra is freely available at https://doi.org/www.megabionet.org/QuaPra/.

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Acknowledgements

This work was supported by the National High Technology Research and Development Program of China (2015AA020108), the National Key Research and Development Program of China (2016YFC0902100), the China Human Proteome Project (2014DFB30010 and 2014DFB30030), the National Science Foundation of China (31671377, 31401133, 31771460 and 91629103) and the Program of Introducing Talents of Discipline to Universities of China (B14019). We thank Dr. Jiannan Lin, Huanlong Liu, Yimin Ma, Yan Shi, Jiwei Chen, Jun Tang, Qing Zhou for their extensive help with this manuscript. Thanks for the Graduate School and Supercomputer Center of East China Normal University.

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Correspondence to Geng Chen or Tieliu Shi.

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Ji, X., Tong, W., Ning, B. et al. QuaPra: Efficient transcript assembly and quantification using quadratic programming with Apriori algorithm. Sci. China Life Sci. 62, 937–946 (2019). https://doi.org/10.1007/s11427-018-9433-3

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Keywords

  • RNA-Seq
  • transcriptome reconstruction
  • transcript assembly
  • transcript quantification