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COSINE: non-seeding method for mapping long noisy sequences.

Pegah Tootoonchi Afshar1, Wing Hung Wong2

  • 1Department of Electrical Engineering, School of Engineering, Stanford University, Stanford, CA 94305, USA.

Nucleic Acids Research
|June 7, 2017
PubMed
Summary
This summary is machine-generated.

Third generation sequencing (TGS) produces long, error-prone reads. COSINE is a new alignment method that effectively handles these noisy sequences, improving accuracy for genomic analysis.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Third generation sequencing (TGS) technologies offer long reads but are hampered by high error rates.
  • Existing sequence alignment algorithms struggle with the noise and length of TGS reads.
  • Accurate read alignment is crucial for various genomic applications.

Purpose of the Study:

  • To introduce COSINE, a novel alignment method specifically designed for long, error-prone sequencing reads.
  • To evaluate the performance of COSINE against existing alignment tools.
  • To demonstrate the utility of COSINE in handling high error rates characteristic of TGS data.

Main Methods:

  • COSINE calculates sequence similarity based on the distribution of short k-mers (k=3-4).
  • It measures context similarity between stretches of nucleobases.
  • The method was tested using both simulated and real sequencing data.

Main Results:

  • COSINE demonstrates high sensitivity and specificity across a range of read accuracies.
  • The method significantly outperforms existing alignment techniques when error rates are high.
  • COSINE effectively addresses the challenges posed by noisy TGS reads.

Conclusions:

  • COSINE provides a robust solution for aligning long, error-prone sequencing reads.
  • This method offers substantial advantages for analyzing data from third generation sequencing technologies.
  • COSINE enhances the utility of TGS data in genomic research.