Supporting code for manuscript: "Human gut prophages alleviate colitis through immunomodulatory oligosaccharide biosynthesis"

This repository contains computational workflows for prophage identification and downstream analysis from metagenomic data.

Table of Contents

1. Basic Pipeline

   The core pipeline for prophage detection consists of the following steps:

   1. Quality Control and Assembly
   2. Contig Filtering
   3. Prophage Detection
   4. Coverage-Based Prophage Activity Evaluation
   5. Metagenome Binning and Taxonomic Assignment

2. UHGG

   R script for generating Fig 1, Fig s1-s2.

3. Public Metagenome

   R script for generating Fig 2-3.