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Assembly scaffolding with PE-contaminated mate-pair libraries.

Kristoffer Sahlin1, Rayan Chikhi2, Lars Arvestad3

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Summary

This study introduces a new method to handle PE-contamination in mate-pair libraries, improving genome assembly scaffolding. The enhanced scaffolder BESST significantly reduces misassemblies caused by this common library issue.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genome scaffolding orders and orients DNA contigs using paired-end and mate-pair libraries.
  • PE-contamination, where read pairs have incorrect orientation and insert size, complicates scaffolding.
  • Existing scaffolding methods struggle with PE-contamination, as orientation is not always detectable.

Purpose of the Study:

  • To address and model PE-contamination in mate-pair libraries for improved genome scaffolding.
  • To evaluate the impact of PE-contamination on scaffolding quality and the effectiveness of a new modeling approach.

Main Methods:

  • Developed an integer linear programming formulation to model PE-contamination.
  • Implemented the model in an updated version of the scaffolder BESST.
  • Utilized an efficient heuristic to solve the optimization problem.

Main Results:

  • The updated BESST demonstrates significant improvements over existing integrated and stand-alone scaffolders.
  • Quantified the positive impact of modeling PE-contamination compared to previous BESST versions.
  • Showcased the vulnerability of other scaffolders to PE-contaminated libraries, leading to more misassemblies and inflated assembly sizes.

Conclusions:

  • Modeling PE-contamination is crucial for accurate and reliable genome scaffolding.
  • The enhanced BESST provides a robust solution for handling PE-contaminated libraries.
  • This work advances the field of genome assembly by addressing a critical practical challenge.