oxo-call: Documentation-grounded Skill Augmentation for Accurate Bioinformatics Command-line Generation with Large Language Models

TL;DR

oxo-call is a bioinformatics command-line assistant that uses documentation grounding and skill augmentation with large language models to generate accurate tool commands, supporting reproducibility and privacy.

Contribution

It introduces a new approach combining documentation grounding and domain-specific skill augmentation for LLM-based bioinformatics command generation.

Findings

Ships over 150 skills across 44 analytical categories.

Supports local LLM inference for privacy.

Provides a DAG workflow engine and extensibility features.

Abstract

Command-line bioinformatics tools remain essential for genomic analysis, yet their diversity in syntax and parameterization presents a persistent barrier to productive research. We present oxo-call, a Rust-based command-line assistant that translates natural-language task descriptions into accurate tool invocations through two complementary strategies: documentation-first grounding, which provides the large language model (LLM) with the complete, version-specific help text of each target tool, and curated skill augmentation, which primes the model with domain-expert concepts, common pitfalls, and worked examples. oxo-call (v0.10) ships >150 built-in skills covering 44 analytical categories, from variant calling and genome assembly to single-cell transcriptomics, compiled into a single, statically linked binary. Every generated command is logged with provenance metadata to support reproducible research. oxo-call also provides a DAG-based workflow engine, extensibility through user-defined and community skills via the Model Context Protocol, and support for local LLM inference to address data-privacy requirements. oxo-call is freely available for academic use at https://traitome.github.io/oxo-call/.