biobox: A Bioinformatics Toolbox

Bioinformatics teams often find themselves reinventing the wheel: dozens of small scripts for trimming adapters, running quality control or generating plots live in disparate places.
Over time this leads to duplicated effort and inconsistent quality.
The Bioinformatics Toolbox provides a standardized collection of modules analogous to projects like nf-core/modules and snakemake-wrappers -- but implemented as Viash components.
Each module is self-contained, versioned and containerized so that it can run on its own or be composed into larger workflows.

Who is it for?

This library is designed for computational biologists, platform engineers and anyone responsible for maintaining a suite of pipelines.
If you need to share tools across teams or modernize fragile scripts into reusable pieces, the Toolbox offers a clear path.

What's Inside?

Here are a few examples of components included in the Toolbox:

  • FASTQ Quality Control -- wraps FastQC to generate per-sample QC reports and integrates with MultiQC for aggregate summaries.
  • Genome Alignment -- wrappers around STAR and BWA with sensible defaults and support for UMI handling.
  • Expression Quantification -- modules running Salmon, Kallisto or RSEM for transcript abundance estimation.
  • Visualization & Plotting -- stand-alone tools for generating gene expression heatmaps, PCA plots and summary statistics.

Each module exposes a consistent command-line interface and ships with its own container image.
You can run these tools individually or plug them into existing workflows.

Compliance & Portability

All Toolbox components are built with compliance and portability in mind.
Versioned containers and automatically generated SBOMs (Software Bill of Materials) ensure that every run is auditable and reproducible.
Because Viash components run on any infrastructure -- whether local, HPC or cloud -- adopting the Toolbox does not lock you into a single platform.