Jan2024 reference datasets for Mitohelper

Reference datasets (Jan 2024 update) for Mitohelper (https://github.com/aomlomics/mitohelper)

Dec 2023 update: COI dataset was cleaned up in Dec2023 to remove non-COI records.

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.Jan2024.tsv (839,731 records)

mitofish.12S.Jan2024.tsv (54,390 records)

mitofish.12S.Jan2024_NR.fasta (FASTA file of 12S rRNA gene records)

mitofish.COI.Jan2024.tsv (306,475 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