Resources and Databases for Amplicon Metagenomics
Updated on: 03 Sep 2019
- 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
- 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
- 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
- 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
- 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
- UNITE
- Description: UNITE is a web-based database and sequence
management environment for the molecular identification of
fungi.
- Link: https://unite.ut.ee
- 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
- 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
- MicrobiomeDB
- 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
- 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
- Specific Microbiome Projects
- 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
- 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
- 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
- Open research data and software
- Open Tree of Life
- IMR - Integrated Microbiome Resource
- Description: The Integrated Microbiome Resource provides
extensive expertise and knowledge on microbiome sequencing and
bioinformatics.
- Link: https://imr.bio
[microbiome
amplicon-metagenomics
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