The primary objective of this guide is to summarize all of the popular approaches for boosting the execution speed of your Python code.
Resources and Databases for Amplicon Metagenomics
- 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
- 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
- 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
- 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
- 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
- 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
- Description: MicrobiomeDB is a data-mining platform for interrogating microbiome experiments
- Link: https://microbiomedb.org/mbio/app
- 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
- Description: List of different microbiome projects/resources/databases.
- Link: http://themicrobiome.com/en/about/more/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
- 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
- Description: Include links for:
- Machine learning and ecological models
- Microbial ecology (tutorials and packages)
- Link: https://openresearchlabs.github.io/code
- Description: Include links for:
- 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
- IMR - Integrated Microbiome Resource
- Description: The Integrated Microbiome Resource provides extensive expertise and knowledge on microbiome sequencing and bioinformatics.
- Link: https://imr.bio
A curated list of articles, tutorials and workshops for microbiome data processing and analysis, and more.
A curated list of list of software, web-apps and R/Python packages, which can be used in microbiome research, and more.
A curated list of various databases and online resources, which can be useful in microbiome research.
List of valuable literature papers for microbiome research.