| NCBI RefSeq |
Comprehensive, curated collection of reference sequences, including genomes for taxonomy. |
39526381 |
| MARMICRODB |
Database for taxonomic classification of (marine) metagenomes. |
zenodo |
| MGnify Database |
Database for microbiome-derived sequences with taxonomic annotations and analysis tools. |
36477304 |
| IMG |
Integrated genome and metagenome database. |
22194640 |
| IMG/PR |
A database of plasmids from genomes and metagenomes with rich annotations and metadata. |
37930866 |
| IMG/VR |
An expanded database of uncultivated virus genomes. |
36399502 |
| Kraken2 Database |
Database tailored for use with Kraken2, optimized for fast and accurate metagenomic assignments. |
31779668 |
| NMPFamsDB |
A database of novel protein families from microbial metagenomes and metatranscriptomes. |
37811892 |
| SILVA |
Ribosomal RNA database for taxonomy and phylogenetics, widely used for microbial studies. |
23193283 |
| RDP (Ribosomal Database Project) |
High-quality ribosomal RNA sequences for taxonomy and functional annotations. |
24288368 |
| Greengenes |
16S rRNA database for microbial taxonomy and phylogeny (limited updates). |
16820507 |
| GTDB |
A standardized bacterial and archaeal taxonomy based on phylogenomics. |
34520557 |