MIDORI REFERENCE
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Quality controlled, preformatted, and regularly updated

Reference databases for taxonomic assignment of eukaryotic mitochondrial sequences

MIDORI Reference provides quality-controlled DNA and amino acid reference sequences for taxonomic assignment, metabarcoding, and mitochondrial biodiversity studies.

Sequences for taxonomic assignment
A T G C G A A T C T G A T C G A A G T C
A T G C G A A T C T G A T C G A A G T C
TACGCTTAGACTAGCTTCAG
TACGCTTAGACTAGCTTCAG
15 mitochondrial genes
9 available formats
2 sequence types

MIDORI Reference workflow

All Eukaryota Expanded beyond Metazoa to include eukaryotic diversity.
DNA and amino acids Nucleotide databases and translated protein databases.
Regularly updated Versioned with successive GenBank releases.
Available database formats

Select a format that fits your preferred taxonomic assignment pipeline.

RDP

RDP Classifier

Formatted for taxonomic classification using the RDP Classifier.

Learn about RDP
M

MOTHUR

Reference files for sequence classification in MOTHUR workflows.

Learn about MOTHUR
Q2

QIIME 2

Compatible reference data for QIIME 2 feature-classifier workflows.

Learn about QIIME 2
SP

SPINGO

Preformatted databases for rapid sequence-based taxonomic assignment.

Learn about SPINGO
SX

SINTAX

Reference sequences prepared for SINTAX classification in USEARCH.

Learn about SINTAX
D2

DADA2

Reference data for taxonomy assignment in DADA2 analysis pipelines.

Learn about DADA2
BL

BLAST+

Searchable databases for alignment-based sequence identification.

Learn about BLAST+
K2

Kraken2

Reference databases for k-mer-based classification with Kraken2.

Learn about Kraken2
FA

RAW FASTA

Original FASTA sequences with taxonomy for custom workflows.

Available database structures

Use a compact database for speed, or preserve more sequence diversity for detailed analyses.

LONGEST

One representative per species

Contains the single longest sequence available for each species.

  • Compact reference database.
  • Efficient taxonomic assignment.
  • Reduced sequence redundancy.
UNIQUE

All unique haplotypes

Contains all unique sequences associated with each species.

  • Preserves sequence-level diversity.
  • Useful when haplotype variation matters.
  • Supports detailed comparisons.
TOTAL

All available sequences

Includes all sequences before collapsing and is available for RAW databases.

  • Maximum sequence representation.
  • Useful for custom analyses.
  • Available through RAW downloads.

MIDORI Reference is under Creative Commons Attribution 4.0 International (CC BY 4.0) license.

GenBank-derived records are provided under their original accessions and subject to the NCBI usage policies .