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HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads.

Stefano Beretta1, Murray D Patterson2, Simone Zaccaria3

  • 1Department of Informatics, Systems, and Communication, University of Milano-Bicocca, Milan, Italy.

BMC Bioinformatics
|July 5, 2018
PubMed
Summary

This study introduces HapCHAT, a new method for haplotype assembly using long sequencing reads. HapCHAT effectively handles higher coverages, improving accuracy and reducing computational resources for more reliable genome analysis.

Keywords:
Haplotype assemblyHigh coverageLong readsMinimum error correctionSingle individual haplotyping

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Haplotype assembly assigns variant alleles to two genome haplotypes.
  • Long reads improve haplotype assembly by spanning more variants but have high error rates.
  • Current methods for long reads struggle with high-coverage datasets.

Purpose of the Study:

  • To develop a novel haplotype assembly method for long reads that accommodates higher coverages.
  • To improve the accuracy and efficiency of haplotype assembly by dynamically adapting error correction.
  • To reduce computational demands for analyzing large sequencing datasets.

Main Methods:

  • A new algorithm combining and extending previous approaches for long-read haplotype assembly.
  • Dynamic adaptation of error estimation at variant sites.
  • Minimization of total error corrections for feasible solutions.

Main Results:

  • The developed tool, HapCHAT, handles higher coverages effectively.
  • Experimental analysis shows improved accuracy and recall with increased coverage.
  • Significant reduction in computational runtimes observed for higher coverage datasets.

Conclusions:

  • The method leverages long-range sequencing information for fewer haplotype blocks.
  • Higher coverage enables better error correction and more accurate haplotype reconstruction.
  • HapCHAT offers an efficient solution for complex haplotype assembly tasks.