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KnuttBinPhylo

The bin (metagenome-assembled genomes/MAG) phylogenetic analysis pipeline

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/KnuttBinPhylo.git
cd KnuttBinPhylo

snakemake -prj 16 --use-conda paper 2>&1 | tee run.log

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The bin (metagenome-assembled genomes/MAG) phylogenetic analysis pipeline

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