• Input: DRAM annotations file.
• Output: distillate (gene presence/absence), product (reaction % presence) and product refined (pathway calls).

Each pathway (e.g. Calvin-Benson carbon fixation) is defined as a combination of reactions (e.g. RubisCO). For a genome to have a positive pathway call, it must have >60% of the total pathway (accounting for alternate reaction paths), it must have some presence in >70% of the reactions (at least one gene) and, it must have the signature genes, where applicable (used to distinguish pathways with high overlap, e.g. the Wood-Ljungdahl methanogenic pathway and hydrogenotrophic methanogenesis).

• Create conda environment: conda env create --name DRAM_product_refined -f environment.yaml.
• Activate environment: conda activate DRAM_product_refined.
• Add path to DRAM annotations to the config in config/config.yaml.
• Run pipeline: snakemake -j 30.