Snakemake workflow: mg_annotate

A Snakemake workflow to annotate mags

Usage

1. Make sure you have conda, mamba and snakemake installed.

   conda --version
   snakemake --version
   mamba --version

2. Clone the git repository in your terminal and get in:

   git clone git@github.com:3d-omics/mg_annotate.git
   cd mg_annotate

3. Test your installation.

   snakemake -np

4. Run it with your own data:

   1. Edit config/features.yml with reference databases:

   # All fastas should be called .fa.gz
   mag_catalogue_dir: resources/mag_catalogue/
   
   databases:
     checkm2: resources/databases/checkm2/20210323/uniref100.KO.1.dmnd
     dram: resources/databases/dram/20230811
     gtdbtk: resources/databases/gtdbtk/release214

   2. Edit config/params.yml with execution parameters. The defaults are reasonable.

5. Run the pipeline

   snakemake \
      --use-conda \
      --profile profile/default \
      --cores 24 \
      --jobs 8 \
      --keep-going \
      --rerun-incomplete

Rulegraph

Features

• Dereplication with dRep. Multiple secondary ANIs can be provided.
• Annotation with checkm2, gtdbtk and dram

References

• dRep
• GTDB-TK
• DRAM
• checkm2