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
The snakemake pipeline is continuously built by GitHub Actions on every change, and OPAL reports are 605A 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.
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 camiThese are other tools which participated in CAMI before and made their submission process public.