Useful External Resources
This page contains links to other websites or educational materials related to the microbiome that users may find helpful.
- 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.
- 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
Review papers on metagenomics analysis methods
- 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