iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline

🦠 📓 a microbiome paper

Meta-analysis of metagenomes via machine learning and assembly graphs reveals strain switches in Crohn’s disease

The scripts contained in this repository relate directly to the work conducted by the Tree Root Microbiome Project (TRMP) led by Dr Steve Wakelin.

MetaTrinity is a novel metagenomic analysis tool employing efficient containment search techniques and heuristics for read mapping to achieve significant speedup while maintaining high accuracy. This positions MetaTrinity as an efficient solution, optimally balancing speed and precision in metagenomic analysis.

Code for reproducing results published in the paper: "Consistent changes in the intestinal microbiota of Atlantic salmon fed insect meal diets"

MicrobioSee2, a desktop sofware for visulization of microbiome result, which contian multiple modules, such as Alpha Diversity, Beta Diversity, Species Conpositions, volcano plot, and pie chart.

This repository presents the files and methods used for statistical analyses of the faecal bacterial community profiles and SCFA data generated from calves raised on three different allowances of milk replacer.

QUOR'EM: Query, Update, Organize, and Render 'EM

This website gives an introduction to microbial community analysis.