Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
- Snakemake
- Prodigal
- Diamond
- R
You will need a diamond index of UniProt TREMBL
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
snakemake --use-conda --cores 1 create_ref
snakemake --use-conda --cores 1 all