KnuttBinAnno

Throw a bunch of annotation tools and pipelines at your bins (MAGs).

This is the version of the pipeline as it was used for the paper. Some data outputs weren't used and have been disabled.

Setup

This pipeline requires a lot of disk space for its reference databases (~200GB)

1. Install the latest version of a conda distribution and Snakemake (>=5.10)
2. Clone this repository (paper branch)
3. Copy the bins into the input folder (ending in .fa)
4. Run the paper rule with conda enabled

conda create -y -n snake -c bioconda -c conda-forge snakemake>=5.10
conda activate snake
git clone -b paper https://github.com/KnuttPipeline/KnuttBinAnno.git
cd KnuttBinAnno

snakemake -prj 16 --use-conda paper 2>&1 | tee run.log
# Run with 16 cores available