Home

SAMWISE title

SAMWISE is a semi-automated, end-to-end metagenomic read processing program implemented as a collection of Nextflow DSL2 workflows.

SAMWISE workflow

The workflows support read validation and trimming, assembly, binning, bin refinement, MAG annotation, metabolic-model generation, and selected auxiliary analyses. SAMWISE can be run without the optional AI agent.

Choose a path¶

Install the prerequisites before running a workflow.
Follow the quick start for a representative end-to-end run.
Review input preparation before supplying reads.
Use the workflow reference for module-specific behavior and options.
Read about the optional AI agent separately before configuring credentials.

Source and license¶

The source repository is available at PNNL-SoilSFA/samwise. See the repository's LICENSE.md for licensing and government disclaimer terms.

The documentation is being organized from the root README.md. The root README remains unchanged during this parity review; the Zensical pages are being expanded to provide the complete workflow reference before any README cleanup.