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Synopsis

detectEVE is an open-source Snakemake tool designed for the fast and precise detection of nrEVEs in genomic assemblies, offering high user flexibility.

 # download workflow
git clone https://github.com/thackl/detectEVE
cd detectEVE

# install dependencies via conda or mamba (https://github.com/conda-forge/miniforge)
mamba create -n detectEVE
mamba activate detectEVE
mamba env update --file workflow/envs/env.yaml

# run detectEVE
./detectEVE -h                       # show help
./detectEVE [options] [<in.fa> ...]  # analyze local fasta files
./detectEVE [options] -a acc.csv     # download & analyze NCBI accession table
./detectEVE [options] -A acc,acc     # download & analyze NCBI accession list

# or combine local fasta files and remote accessions
./detectEVE [options] [(-a acc.csv | -A acc,acc)] [<in.fa> ...]

# download and prep databases
./detectEVE --setup-databases [--snake ARGS]

# run example data
cd examples
../detectEVE *.fna