Useful External Resources

This page contains links to other websites or educational materials related to the microbiome that users may find helpful.

Web Apps

• MicrobiomeDB is a data-mining platform for interrogating microbiome experiments. It is part of the EuPathDB family of NIAID-funded bioinformatics resource centers.
• Calypso is for amplicon downstream analysis.
• MetaboAnalyst is for metabolomics analysis and can integrate microbiome data, including results from their sister tool MicrobiomeAnalyst.
• EBI has tools for multiple sequence alignment, some of which work with up to 4mb files for MSA and can be used with their phylogeny tools for tree construction.
• MG-RAST is a (WGS) metagenomics analysis server.
• QIIME 2 View page is for viewing .qza and .qzv files output by QIIME 2.
• Taxonomer metagenomics app is for taxonomic assignment.
• Huttenhower Lab's Galaxy server has tools specifically for microbiome analysis.
• MGnify from EMBL-EBI has tools for searching their databases of publicly available microbiome data, as well as for analyzing the public data or your own datasets.
• SILVA provides databases for 16S/18S and 23S/28S rRNA sequences, and SILVAngs for analysis of amplicon NGS data.
• eHOMD provides databases and tools for analysis of the Human Oral Microbiome.
• METAGENOTE is for organizing and annotating data from genomics studies, including microbiome. It also allows for easy submission of the data and metadata to SRA.
• Piphillin is a webserver from Second Genome which provides prediction of metagenomic content by direct inference from 16S results using KEGG and BioCyc databases.

Software tools and downloads

• Pavian is an R shiny app for visualizing and comparing metagenomics results. To use with MetaPhlAn2/bioBakery results, you will need to edit the header of the taxonomic profile to remove the comment character #.
• Microbiome analysis software developed by EMBL
• Second Genome's archive of the Greengenes database
• MaAsLin2 is a Bioconductor package for determining multivariate associations between metadata and meta'omic datasets using linear models.

Tutorials

• phyloseq is an R meta-package for analysis of microbiome data which ties together other R packages for ease of use. They have many tutorials on their site, in particular:
  • DESeq2 and edgeR for assessing differential abundance
  • Bar plots using ggplot2
• QIIME 2 Tutorials

Educational Material

• Review papers on metagenomics analysis methods
  • Tools for Analysis of the Microbiome
  • Current understanding of the human microbiome
  • Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases
• Training videos
  • Metagenomics analysis overview - These are videos from live training sessions offered to students of Makerere University in Uganda as a supplement to their course work learning
  • Part 1: 16S analysis
  • Part 2: WGS analysis