Other databases and resources
Other databases
Maintaining reference databases requires accurate and high-quality sequence data, as well as meticulous annotation and regular updates to reflect the rapidly expanding knowledge of bio diversity. Taxonomic annotation of sequencing data is provided in the following databases:
- UNITE database
- based on the ITS region covers all eukaryotes with the main focus on Fungi
- SILVA database
- includes SSU and LSU genes, from both amplicons and (meta)genomes
- PR2 database
- includes the SSU gene and mainly focuses on protists
- 18S-Nemabase
- focuses on SSU gene of nematode
- BOLD
- focus on COI of animals
- MIDORI
- Eukaryota mitochondrial DNA sequences
In comparison with the above databases, the EUKARYOME utilizes additionally long reads spanning the SSU, ITS, and LSU regions, which would be essential for chimera filtering and improved identification using ultra-long reads.
Software:
- PipeCraft2 – metabarcoding data analyses platform with graphical user interface; best for custom solutions.
- NextITS – metabarcoding data analyses pipeline for full-length ITS sequences from PacBio sequencers (integrated also in PipeCraft2).
Other resources
- The Global Soil Mycobiome consortium (GSMc) – global soil SSU-V9 + ITS dataset for all eukaryotes
- FungalTraits ecological traits database for fungi and fungi-like stramenopiles
- PlutoF – platform for metadata and taxonomic annotation and data curation
- WoRMS – taxonomy and classification of marine biota
- NeMys – ecological traits database for nematodes
- UniEuk – sequence and taxonomic resource for all eukaryotes, focus on marine protists
