Oct2023 reference datasets for Mitohelper

Reference datasets (Oct2023 update) for Mitohelper (https://github.com/aomlomics/mitohelper)

Major update (Nov2022): The 12S rRNA gene sequence dataset is now filtered to only contain mitochondrial genomes annotated with 12S rRNA gene sequences. Sequences of the 12S rRNA gene are now extracted from complete mitochondrial genomes to construct a more gene-specific 12S rRNA dataset. 12S rRNA gene sequences in mitohelper's dataset are available for download as mitofish.12S.$month$year_NR.fasta

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.Oct2023.tsv (829,196 records)
• mitofish.12S.Oct2023.tsv (51,512 records)
• mitofish.12S.Oct2023_NR.fasta (FASTA file of 12S rRNA gene records)
• mitofish.COI.Oct2023.tsv (339,894 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