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Ish: Alineación local y semi-global acelerada por SIMD y GPU como herramienta de filtrado CLI

¹Life Sciences Group, Bio-Rad Laboratories, Hercules, CA 94547, United States.

Bioinformatics advances

|February 26, 2026

Abstracto

Motivation:

To date, there has been no command line utility for performing index-free alignment-based filtering of records. Since filtering using command line tools is a staple of Bioinformatics, this leaves a gap in command line workflows.

Results:

Ish is the first composable unix-style command line tool for filtering the input target records to only those that match the input query with a threshold alignment score, using a selectable alignment algorithm and selectable record type. The core alignment algorithms for ish meet or exceed the performance of their reference implementations in Parasail for both SIMD and GPU alignment, as measured by gigacell updates per second (GCUPs).

Availability And Implementation:

The source code and documentation are available at https://github.com/BioRadOpenSource/ish under the Apache-2.0 License and open for community contributions. Ish is installable with Conda and supports Linux and macOS.

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