Welcome to MiFoDB

MiFoDB is a workflow designed for the alignment-based profiling of microbes associated with microbial foods. This workflow includes instructions on how to analyze your own fermented food samples from the raw sequencing data to profiling the results and downstream analysis. We inlude a tripartite database (MiFoDB), as well as details to expand and/or build your own an alignment based database.

In addition to high accuracy and low false positive profiling results, MiFoDB’s incorporation into the InStrain (Olm et al. 2021) framework allows for strain tracking, functional analysis, and gene profiling within the same workflow.

Check out the Overview section for further information.

Note

This project is under active development.

Comments and suggestions can be sent to Elisa Caffrey.

Contents

• Overview
  • The MiFoDB Workflow
  • Why use alignment-based profiling?
  • Which microbes are included in MiFoDB?
  • What can I do with MiFoDB results?
  • Why don’t I have 100% mapping?
  • Run Time Information
• Quick Start
  • Pre-processing with nextflow
  • Profile with nextflow
• Step-By-Step Guide
  • Pre-processing
  • Profiling
• Example Output
  • Table setup
  • Calculate relative abundance:
• Advanced Use
  • Creating a custom MiFoDB
  • Adding MAGs to database
  • Functional Analysis and Gene Profiling
  • Strain Tracking
• Acknowledgements
  • People
  • Citation