Identification of NRPS and PKS gene clusters, including the pks island, in bacterial metagenome from CRCbiome

This repository contains all code and scripts developed for the master's thesis "Identification of NRPS and PKS gene clusters, including the pks island, in bacterial metagenome from CRCbiome".

Three Snakemake-based pipelines have been developed. For detailed description of each pipeline, please refer to the links below.

1. MAG-based identification of BGCs (not executed).
2. MAG-based identification of BGCs.
3. Read-based identification of the pks island and E. coli.

The programming language R have been used for data analysis after running the pipelines. R scripts can be accessed here.