Formatting sourmash for CAMI evaluations

This repo has the snakemake pipeline for running CAMI 2 evaluations (with OPAL), including indices preparation based on the CAMI 2 databases.

The sourmash biobox definition is currently in sourmash-bio/bioboxes

Examples

The snakemake pipeline is continuously built by GitHub Actions on every change, and OPAL reports are published to github pages. Here are the links to access them:

• CAMI I low complexity challenge dataset: Metalign results from their repo, results for other tools come from the OPAL repo.
• CAMI II mouse gut toy dataset: I ran Metalign based on the setup instructions and running with example data wiki pages, and other tools results are from the official data repository for the CAMI 2 challenges.

Setup

All processing and analysis scripts were performed using the conda environment specified in environment.yml. To build and activate this environment run:

conda env create --force --file environment.yml

conda activate cami

Other similar CAMI evaluation repos

These are other tools which participated in CAMI before and made their submission process public.

• CCMetagen