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Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
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PaSS: a sequencing simulator for PacBio sequencing.

Wenmin Zhang1, Ben Jia1, Chaochun Wei2,3

  • 1Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.

BMC Bioinformatics
|June 23, 2019
PubMed
Summary
This summary is machine-generated.

A new PacBio Sequencing Simulator (PaSS) was developed to accurately model third-generation sequencing data. PaSS outperforms existing tools, generating simulated reads closely resembling experimental data for bioinformatics tool development.

Keywords:
Next generation sequencingPacBio sequencingSequence patternSequencing errorSequencing simulatorThird generation sequencing

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Third-generation sequencing (TGS) platforms like PacBio offer longer reads than second-generation sequencing (NGS).
  • PacBio sequencing exhibits unique error patterns, necessitating specialized bioinformatics tools.
  • Effective read simulators are crucial for developing and validating these tools.

Purpose of the Study:

  • To develop an advanced PacBio sequencing simulator capable of learning sequence patterns from real data.
  • To create a simulator that incorporates context-specific error models beyond simple error rate distributions.
  • To provide a tool that generates highly realistic simulated PacBio reads for bioinformatics analysis.

Main Methods:

  • Development of the PacBio Sequencing Simulator (PaSS) software.
  • Incorporation of a context-specific sequencing error model.
  • Learning sequence patterns directly from available PacBio sequencing data.

Main Results:

  • PaSS demonstrates superior performance compared to existing simulators like PBSIM, LongISLND, and NPBSS.
  • Simulated reads from PaSS exhibit high similarity to experimental PacBio sequencing data, confirmed by assembly tests.
  • The simulator accurately models read length distributions and error rates, including context-specific errors.

Conclusions:

  • PaSS is an effective and accurate simulator for PacBio sequencing data.
  • This tool will significantly aid in the evaluation and development of novel bioinformatics tools for TGS data analysis.
  • PaSS enhances the reliability of simulated data for benchmarking and improving genomic analysis pipelines.