10 Building or using custom reports

Adding Your Own Custom Analysis to the BGCFlow Report

As mentioned in the previous chapter, one of the core features of BGCFlow is its support for custom reports, a powerful aspect that allows users to tailor their analyses to meet specific research needs.

Custom reports let you focus on the BGC aspects most relevant to your work. Whether you're interested in specific types of natural products, comparing BGCs across species, or uncovering new BGCs, custom reports provide the tools you need to dig deeper into your data. And what's more important, is that you can share it the resulting report with your colleagues or community and make it reproducible.

BGCFlow custom reports were inspired by the article Reproducible Reports with MkDocs by Tim Vink. Under the hood, it combines Jupyter Notebook and Material for MkDocs.

Getting Started with Custom Reports

We have prepared a detailed tutorial that walks you through the process of creating a custom report focused on identifying unique polyketide BGCs. This tutorial serves as an excellent starting point for learning how to leverage BGCFlow for your custom analyses.

The tutorial is available here: custom_reports

The tutorial consists of two parts:

1. Using Tables to Filter and Identify Unique Polyketide BGCs: This tutorial will guide you through the steps of generating a custom report, from data preparation to simple analysis of BGC filtering and prioritization.

2. Exploring Integrated Network: The second tutorial gives a how to guide for an integrated analysis utilizing networks of knowledge bases from different tools: BiG-SCAPE, antiSMASH KnownClusterBlast, BiG-FAM database query, and ARTS2.

A Real Example Project ‐ Saccharopolyspora Dataset

An example use case of BGCFlow can be seen in the manuscript Nuhamunada, M., O.S. Mohite et al. (2023). This section will explain how to set up the configurations required to generate the dataset which are being used in the analysis of Saccharopolyspora genomes.

1. Download the dataset

• Donwload the dataset containing the BGCFlow runs from Zenodo

# move to bgcflow dir
cd bgcflow

# download and extract dataset
wget https://zenodo.org/record/8018055/files/saccharopolyspora_dataset.zip
unzip saccharopolyspora_dataset.zip

2. Re-run the dataset using the latest BGCFlow version

Make necessary changes to the config file, and run bgcflow:

bgcflow run

Instruction to generate the figures from the manuscript is available at https://github.com/NBChub/saccharopolyspora_manuscript