Resources and Databases for Amplicon Metagenomics

1. ITIS - Integrated Taxonomic Information System
   • Description: ITIS is an online resource where you can find authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world.
   • Link: https://www.itis.gov
2. EukRef [List of Databases]
   • Description: Link is not a direct link to EukRef web sit, but to a web-page within EukRef, which contain information of various rRNA/ITS databases.
   • Link: http://eukref.org/databases
3. FungiDB
   • Description: FungiDB integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining.
   • Link: https://fungidb.org/fungidb
4. SILVA
   • Description: SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).
   • Link: https://www.arb-silva.de
5. Greengenes
   • Description: Greengenes is a full-length 16S rRNA gene database that provides a curated taxonomy based on de novo tree inference.
   • Link: http://greengenes.secondgenome.com
6. UNITE
   • Description: UNITE is a web-based database and sequence management environment for the molecular identification of fungi.
   • Link: https://unite.ut.ee
7. RDP - Ribosomal Database Project
   • Description: RDP provides quality-controlled, aligned and annotated Bacterial and Archaeal 16S rRNA sequences, and Fungal 28S rRNA sequences, and a suite of analysis tools to the scientific community.
   • Link: https://rdp.cme.msu.edu/index.jsp
8. EzBioCloud
   • Description: EzBioCloud is ChunLab’s public data and analytics portal focusing on taxonomy, ecology, genomics, metagenomics, and microbiome of Bacteria and Archaea.
   • Link: https://www.ezbiocloud.net
9. MicrobiomeDB
   • Description: MicrobiomeDB is a data-mining platform for interrogating microbiome experiments
   • Link: https://microbiomedb.org/mbio/app
10. Qiita
    • Description: Qiita (canonically pronounced cheetah) is an entirely open-source microbial study management platform. It allows users to keep track of multiple studies with multiple ‘omics data.
    • Link: https://qiita.ucsd.edu
11. Human Microbiome Project
    • Description: The Human Microbiome is the collection of all the microorganisms living in association with the human body.
    • Link: https://www.hmpdacc.org
12. Specific Microbiome Projects
    • Description: List of different microbiome projects/resources/databases.
    • Link: http://themicrobiome.com/en/about/more/specific-microbiome-projects
13. HPMCD - Human Pan Microbial Communities Database
    • Description: HPMCD. Provides a manually curated, searchable, metagenomic resource to facilitate investigation of human gastrointestinal microbiota.
    • Link: http://www.hpmcd.org
14. Disbiome
    • Description: Disbiome® is a database covering microbial composition changes in different kinds of diseases, managed by Ghent University.
    • Link: https://disbiome.ugent.be/home
15. eHOMD - Human Oral Microbiome Database
    • Description: The expanded Human Oral Microbiome Database (eHOMD) is a comprehensive microbiome database for sites along the human aerodigestive tract that revealed new insights into the nostril microbiome.
    • Link: http://www.homd.org
16. Open research data and software
    • Description: Include links for:
      • Machine learning and ecological models
      • Microbial ecology (tutorials and packages)
      • etc.
    • Link: https://openresearchlabs.github.io/code
17. Open Tree of Life
    • Description: The Open Tree of Life is an online phylogenetic tree of life - a collaborative effort, funded by the National Science Foundation.
    • Link: https://tree.opentreeoflife.org/opentree
18. IMR - Integrated Microbiome Resource
    • Description: The Integrated Microbiome Resource provides extensive expertise and knowledge on microbiome sequencing and bioinformatics.
    • Link: https://imr.bio