ideel

Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes

Dependencies:

• Snakemake
• Prodigal
• Diamond
• R

You will need a diamond index of UniProt TREMBL

Install

Clone the repo.

git clone https://github.com/mw55309/ideel.git

Change directory into the repo folder

cd ideel

Put your genomes (with a ".fa" prefix) in folder genomes

Create all of the conda envs:

snakemake --use-conda --cores 1 --conda-create-envs-only

download the reference DB

snakemake --use-conda --cores 1 create_ref

run

snakemake --use-conda --cores 1 all