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:

  • SILVA database

    • includes SSU and LSU genes, from both amplicons and (meta)genomes
    • last release November 2020
  • UNITE database

    • based on the ITS region covers all eukaryotes with the main focus on Fungi
    • last release October 2022
  •  PR2 database

    • includes the SSU gene and mainly focuses on protists
    • last release May 2023
  • 18S-Nemabase

    • focuses on SSU gene of nematode
  • BOLD

    • focus on COI of animals
  • MIDORI

    • Eukaryota mitochondrial DNA sequences

In comparison with current 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.

 

Other resources

 

  • PlutoF – platform for metadata and taxonomic annotation and data curation
  • INSDc – raw sequence data, associated metadata and taxonomy
  • WoRMS – taxonomy and classification of marine biota
  • FungalTraits ecological traits database for fungi and fungi-like stramenopiles
  • NeMys – ecological traits database for nematodes
  • UniEuk – sequence and taxonomic resource for all eukaryotes, focus on marine protists
  • The Earth Microbiome Project (EMP) – short-read SSU and ITS sequence data for soil eukaryotes
  • The Global Soil Mycobiome consortium (GSMc) – global soil SSU-V9 + ITS dataset for all eukaryotes

 

Software:

  • DADA2 – quality-filtering and clustering platform, best for SSU and LSU amplicons
  • QIIME2 – quality-filtering and clustering platform, best for short SSU and LSU amplicons
  • PipeCraft2 – quality-filtering and clustering platform, best for long reads and custom solutions
  • NextITS – A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio
  • BLAST+ – custom BLAST-searches for taxonomic identification
  • PROTAX-fungi – probabilistic taxonomic placement of fungal ITS sequences
  • RDP Classifier – Naive Bayesian Classifier at all taxonomic levels