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Sequence alignment tools: one parallel pattern to rule them all?

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Summary
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High-level programming simplifies next-generation sequencing (NGS) alignment tools, boosting productivity and performance. This approach abstracts parallelization complexities, enabling comparable or superior results for NGS data analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Software Engineering

Background:

  • Next-generation sequencing (NGS) alignment tools are critical for genomic data analysis.
  • Current parallelization strategies in NGS alignment tools are complex and can hinder productivity.
  • There is a need for improved methodologies to enhance both performance and ease of development.

Purpose of the Study:

  • To advocate for a high-level programming methodology for NGS alignment tools.
  • To improve programmer productivity and achieve absolute performance gains.
  • To demonstrate the effectiveness of a high-level approach in parallelizing NGS alignment.

Main Methods:

  • Analysis of parallel alignment problems and review of existing parallelization strategies in popular NGS alignment tools.
  • Abstraction of these strategies into a single parallel paradigm.
  • Porting alignment tools to the FastFlow pattern-based programming framework.
  • Comparison of performance using high-level parallel patterns.

Main Results:

  • Existing parallelization strategies can be unified under a single paradigm.
  • Porting to the FastFlow framework simplifies parallel programming by managing synchronization and scheduling.
  • High-level parallelization achieved comparable or superior absolute performance across various datasets.
  • Programmers can focus on performance tuning with reduced complexity.

Conclusions:

  • A high-level programming methodology offers significant advantages for developing NGS alignment tools.
  • This approach enhances both programmer productivity and computational performance.
  • FastFlow provides a robust framework for implementing high-level parallel patterns in bioinformatics.