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]