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PSIM: pattern-based read simulator for RNA-seq analysis

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Abstract

Next-generation sequencing technologies (NGS) require mapping tools that are fundamental for their application. These are evaluated by the level of accuracy to be matched and read at the original location. Evaluation increases the need for a simulator to generate reads with their locations and errors, as with indel. In this paper, we propose a simulator, PSIM, that generating a set of artificial RNA segments(reads) with the expression level and errors based on a pattern-based SAM file. PSIM adopts the contour line transpose and interval section shuffle methods to generate a similar expression level. In addition, we show the similarity between a profile contour of synthesized data and a reference sequence.

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Acknowledgments

This research was supported by a grant from the KRIBB Research Initiative Program.

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Authors and Affiliations

  1. Department of Computer Science and Engineering, Pusan National University, Busan, 609-735, Korea

    Sang-min Lee, Haesung Tak, Hwan-Gue Cho & Do-Hoon Lee

  2. Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon, Korea

    Kiejung Park

  3. Korea Institute of Ocean Science and Technology, Ansan, 305-806, Korea

    Kiejung Park

Authors
  1. Sang-min Lee
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  2. Haesung Tak
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  3. Kiejung Park
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  4. Hwan-Gue Cho
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  5. Do-Hoon Lee
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Corresponding authors

Correspondence to Sang-min Lee or Do-Hoon Lee.

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Lee, Sm., Tak, H., Park, K. et al. PSIM: pattern-based read simulator for RNA-seq analysis. Multimed Tools Appl 74, 6465–6480 (2015). https://doi.org/10.1007/s11042-014-2108-x

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  • DOI: https://doi.org/10.1007/s11042-014-2108-x

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