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:

cd workflow
snakemake --cores <cores> --resources gpu=<n_gpus>