generated: '2026-07-18'
method: searched
source: https://software-docs.biomodal.com/en/latest/index.html
name: biomodal CLI
description: >-
  First-party command-line tool that downloads, configures, and runs the biomodal
  duet post-sequencing bioinformatics pipeline (genetic alignment, methylation
  quantification, and variant calling) on the six-base genome data produced by the
  duet evoC and duet +modC multiomics assays.
docs: https://software-docs.biomodal.com/en/latest/index.html
current_version: 2.0.0
legacy_versions:
  - 1.1.3
install:
  method: download-script
  notes: >-
    Downloaded and installed via the biomodal installation script per the software
    documentation hub; the CLI then downloads the duet pipeline itself. Exact
    package-registry distribution (docker/conda/pip) is not published on the public
    docs.
commands:
  - command: biomodal init
    description: Set up configuration files and download the duet pipeline.
  - command: biomodal download
    description: Retrieve new pipeline versions.
  - command: biomodal run duet
    description: Execute the duet post-sequencing pipeline on user FASTQ data.
  - command: biomodal run duet --test
    description: Validate system configuration by running the pipeline against test data.
  - command: biomodal get diagnostics
    description: Gather system and run diagnostics for support.
related:
  - name: modality XPLR
    description: >-
      Separate command-line analysis tool that consumes duet pipeline output for
      deeper methylation exploration, statistics, and visualisation.
  - portal: https://app.biomodal.com
support: support@biomodal.com