intial version

2026-09-17 22:16:42 +01:00
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 # 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>
+```