# eDNA_Stream_E01

## Scope
- Establish whether squiggle-based taxonomy is feasible on the small computational budget that is available

## Dataset:
- NO-MISS bacterial isolates, v10.4.1 chemistry on PromethION flow cells (https://epi2me.nanoporetech.com/nomiss_96bc_p2i_sup_2026/)
    - Downsampling at the pod5 level intended for compute/time reasons -> the full dataset is 293 pod5 / 1.6 TB of raw data 

## Dependencies:
- dorado >= v 2.0.0
- aws CLI
- conda/mamba (mamba recommended)
- python env with:
    - python 3.14
    - snakemake
    - python-dotenv

## Optional:
- .env file with NCBI API key -> slightly speeds up reference fasta download

## Running:
```bash
cd workflow
snakemake --cores <cores> --resources gpu=<n_gpus>
```