MetaWIBELE User Manual

MetaWIBELE (Workflow to Identify novel Bioactive Elements in the microbiome) is a workflow to efficiently and systematically identify and prioritize potentially bioactive (and often uncharacterized) gene products in microbial communities. It prioritizes candidate gene products from assembled metagenomes using a combination of sequence homology, secondary-structure-based functional annotations, phylogenetic binning, ecological distribution, and association with environmental parameters or phenotypes to target candidate bioactives.

Citing MetaWIBELE

If you use the MetaWIBELE software, please cite our manuscript:

Yancong Zhang, Amrisha Bhosle, Sena Bae, Lauren J. McIver, Gleb Pishchany, Emma K. Accorsi, Kelsey N. Thompson, Cesar Arze, Ya Wang, Ayshwarya Subramanian, Sean M. Kearney, April Pawluk, Damian R. Plichita, Gholamali Rahnavard, Afrah Shafquat, Ramnik J. Xavier, Hera Vlamakis, Wendy S. Garrett, Andy Krueger, Curtis Huttenhower*, Eric A. Franzosa*. Discovery of Bioactive Microbial Gene Products in Inflammatory Bowel Disease. Nature, 606: 754–760 (2022)

And feel free to link to MetaWIBELE in your Methods:

http://huttenhower.sph.harvard.edu/metawibele

For additional information, read the MetaWIBELE Tutorial

If you have questions, please direct it to the MetaWIBELE channel of the bioBakery Support Forum.

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Contents

• Workflow
  • Workflow by bypass mode
• Install MetaWIBELE
  • Requirements
  • Installation
    • Install MetaWIBELE
    • Install databases
      • UniRef database
      • Domain database
    • Check install
    • Prepare configuration files
      • Prepare global configuration file
      • Prepare local configuration file
      • Prepare vignette configuration file
• Quick-start Guide
  • How to run
  • Standard Workflows
    • MetaWIBELE-characterize
      • Input files for characterization
      • MetaWIBELE-characterize workflow
      • Demo run of MetaWIBELE-characterize
      • Output files of MetaWIBELE-characterize
    • MetaWIBELE-prioritize
      • Input files for prioritization
      • MetaWIBELE-prioritize workflow
      • Demo run of MetaWIBELE-prioritize
      • Output files of MetaWIBELE-prioritize
• Guides to MetaWIBELE Utilities
  • Preprocessing sequencing reads to build gene families
    • Preprocessing workflow
    • Input files for preprocessing workflow
    • Demo run of preprocessing workflow
    • Output files of preprocessing workflow

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Workflow

Description

MetaWIBELE identifies, prioritizes, and putatively annotates potentially bioactive gene products in host- and non-host-associated microbial communities and human disease phenotypes. This software starts with gene products from assembled metagenomes and combines sequence homology, secondary-structure-based functional annotations, taxonomic profiling, ecological distribution, and environmental or phenotypic association to identify candidate bioactives.

Workflow by bypass mode

There are multiple bypass options that will allow you to adjust the standard workflow.

Bypass options:

• --bypass-clustering
  • do not build protein families
• --bypass-global-homology
  • do not annotate protein families based on global homology information
• --bypass-domain-motif
  • do not annotate protein families based on Interproscan with Phobius/SignalP/TMHMM, Pfam2GO, DOMINE, SIFTS, Expression Atlas database and PSORTb for domain/motif information
• --bypass-interproscan
  • do not annotate protein families based on Interproscan for domain/motif characterization
• --bypass-pfam_to_go
  • do not annotate protein families based on Pfam2GO for domain/motif characterization
• --bypass-domine
  • do not annotate protein families based on DOMINE database for domain/motif characterization
• --bypass-sifts
  • do not annotate protein families based on SIFTS database for domain/motif characterization
• --bypass-expatlas
  • do not annotate protein families based on Expression Atlas database for domain/motif characterization
• --bypass-psortb
  • do not annotate protein families based on PSORTb for domain/motif characterization
• --bypass-abundance
  • do not annotate protein families based on abundance information
• --bypass-mspminer
  • do not annotate protein families based on MSPminer information
• --bypass-maaslin
  • do not annotate protein families based on MaAsLin2 information
• --bypass-integration
  • do not integrate annotations for protein families
• --bypass-mandatory
  • do not prioritize protein families to calculate continuous priority scores
• --bypass-optional
  • do not prioritize protein families based on selecting our for interested annotations (optional prioritization)

Install MetaWIBELE

Requirements

1. Python (version >= 3.6, requiring numpy, pandas, scipy packages; tested 3.6, 3.7)
2. AnADAMA2 (version >= 0.7.4; tested 0.7.4, 0.8.0)
3. CD-hit (version >= 4.7; tested 4.7)
4. Diamond (version >= 0.9.24; tested 0.9.24)
5. MSPminer (version >= 1.0.0; licensed software; tested version 1.0.0)
6. MaAsLin2 (version >= 1.5.1; tested 1.5.1)
7. Interproscan (version >= 5.31-70) (installing with activating Phobius/SignalP/TMHMM analyses; InterProScan 5.51-85.0 or later are recommended for potential simpler installation; tested 5.31-70, 5.51-85.0; you can skip to install Interproscan if you’d like to ignore domain/motif annotation by running MetaWIBELE with “--bypass-interproscan”)
8. Signalp (version >= 4.1; licensed software; installing with integrating in interproscan; used for domain/motif annotation; tested 4.1)
9. TMHMM (version >= 2.0; licensed software; installing with integrating in interproscan; used for domain/motif annotation; tested 2.0)
10. Phobius (version >= 1.01; licensed software; installing with integrating in interproscan; used for domain/motif annotation; tested 1.01)
11. PSORTb (version >= 3.0) (licensed software; used for domain/motif annotation; tested 3.0; you can skip to install psortb if you’d like to ignore protein subcellular localization annotations by running MetaWIBELE with “--bypass-psortb”)
12. Optional: only required if using MetaWIBELE utilities to prepare inputs for MetaWIBELE using metagenomic sequencing reads
    • MEGAHIT (version >= 1.1.3; tested 1.1.3)
    • Prokka (version >= 1.14-dev; recommend to not set '-c' parameter when running prodigal with metagenome mode; tested 1.14-dev)
    • Prodigal (version >= 2.6; tested 2.6)
    • SeqKit (version >= 2.6.1; tested 2.6.1)
    • Bowtie2 (version >= 2.3.2; tested 2.3.2)
    • SAMtools (version >= 1.9; tested 1.9)
    • featureCounts (version >= 1.6.2; tested 1.6.2)

Note: Please install the required software in a location in your $PATH. If you always run with gene families (non-redundant gene catalogs), the optional softwares are not required. Also if you always run with one or more bypass options (for information on bypass options, see optional arguments to the section Workflow by bypass mode). The software required for the steps you bypass does not need to be installed.

Installation

Install MetaWIBELE

You only need to do any one of the following options to install the MetaWIBELE package.

Option 1: Installing with docker

• $ docker pull biobakery/metawibele
• This docker image includes most of the dependent software packages.
• Large software packages and those with licenses are NOT included in this image and needed to be installed additionally:
  • Users should review the license terms and install these packages manually.
  • Softwares with the license : MSPminer, Signalp, TMHMM, Phobius