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seekdeep_nanopore

a basic workflow for running seekdeep on nanopore

Installation:

Install conda with: https://github.com/conda-forge/miniforge#mambaforge

Install snakemake in an environment called snakemake with:

mamba create -c conda-forge -c bioconda -n snakemake snakemake

Usage:

  • Change directory to a folder where you want to run the analysis
  • Download the seekdeep_nanopore_general.smk file into this folder
  • Download the sif file from here into the same folder: https://seekdeep.brown.edu/programs/elucidator.sif
  • Download the seekdeep_nanopore_general.yaml file into the same folder
  • Edit the config.yaml file using the instructions in the comments. Use a text editor that outputs unix line endings (e.g. vscode, notepad++, gedit, micro, emacs, vim, vi, etc.)
  • Activate snakemake with:
conda activate snakemake
  • Run snakemake with:
snakemake -s seekdeep_nanopore_general.smk --cores [your_desired_core_count]