Nephele Tutorials

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


  • 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:
  • QIIME 2 Tutorials

Educational Material