Sep2024 reference datasets for Mitohelper

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

Sep 2024 Update: Double-checked long (>1,000 bp) 12S rRNA sequences and removed flanking non-12S sequences from some 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.Sep2024.tsv (870,372 records)

mitofish.12S.Sep2024.tsv (60,501 records)

mitofish.12S.Sep2024_NR.fasta (FASTA file of 12S rRNA gene records)

mitofish.COI.Sep2024.tsv (316,251 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