Nov2025 reference datasets for Mitohelper

Reference datasets (Nov 2025 update) for Mitohelper (https://github.com/aomlomics/mitohelper)

The MitoFish database underwent a major update since September 30th (UTC + 9) where duplicated records were combined into one entry. The Nov2025 version of Mitohelper's reference datasets was de-deduplicated based on updated records in the September 30th version of the MitoFish database.

Mitohelper is a repository built to facilitate experimental design, alignment visualization, and reference sequence analysis in fish eDNA studies. Refer to our paper and Mitohelper's wiki for database construction pipeline.

I. Reference database files in tab-separated format, containing gene, taxonomy, and sequence information:

• mitofish.all.Nov.2025.tsv (558,313 de-duplicated records)
• mitofish.12S.Mar2025.tsv (64,059 records of 12S rRNA gene >50 bp long)
• mitofish.12S.Mar2025_NR.fasta (FASTA file of 12S rRNA gene records)
• mitofish.COI.Mar2025.tsv (200,911 de-duplicated records)

II. De-replicated QIIME 2-compatible 12S/12S+16S+18S rRNA reference datasets:

• 12S-seqs-derep-uniq.qza
• 12S-tax-derep-uniq.qza
• 12S-16S-18S-seqs.qza
• 12S-16S-18S-tax.qza

If you use Mitohelper, please cite:
Jean Lim, S, Thompson, LR. Mitohelper: A mitochondrial reference sequence analysis tool for fish eDNA studies. Environmental DNA. 2021; 00: 1– 10.  https://doi.org/10.1002/edn3.187