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Ish: SIMD and GPU accelerated local and semi-global alignment as a CLI filtering tool.

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Ish is a new command-line tool for bioinformatics that enables index-free, alignment-based record filtering. It offers high performance, meeting or exceeding existing tools, and is easily installable via Conda.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Command-line tools are essential for bioinformatics workflows.
  • A gap exists for index-free, alignment-based record filtering utilities.
  • Existing methods may lack efficiency or flexibility.

Purpose of the Study:

  • Introduce Ish, a novel command-line tool for sequence record filtering.
  • Address the need for efficient and flexible alignment-based filtering in bioinformatics.
  • Provide a composable, Unix-style utility for command-line workflows.

Main Methods:

  • Developed Ish as a composable, Unix-style command-line tool.
  • Implemented selectable alignment algorithms and record types for flexible filtering.
  • Utilized optimized alignment algorithms (SIMD and GPU) for high performance.

Main Results:

  • Ish is the first tool to offer index-free, alignment-based record filtering via command line.
  • Core alignment algorithms in Ish meet or exceed reference implementation performance (Parasail).
  • Performance measured in gigacell updates per second (GCUPs) for both SIMD and GPU alignment.

Conclusions:

  • Ish fills a critical gap in bioinformatics command-line workflows.
  • The tool provides efficient and flexible sequence record filtering capabilities.
  • Ish is open-source, easily installable (Conda), and supports Linux/macOS.