Introducing Mitohelper, a Python-based mitochondrial reference sequence analysis tool for fish eDNA studies. We built fish reference datasets for 1) all mitochondrial sequences, 2) COI sequences, and 3) 12S rRNA gene sequences by adding gene names and structured taxonomic information to publicly available sequences in the MitoFish database.
getrecord - searches MitoFish for available mitochondrial (cytochrome c oxidase, 12S rRNA, and others) gene sequences against a user-provided list of fish taxonomic names
getalignment - aligns (often partial) mitochondrial gene sequences to a user-specified full-length reference sequence for the assessment and visualization of overlapping sequencing regions
QIIME2-compatible, ready-to-use taxonomic classifiers based on Mitohelper's (MitoFish) 12S rRNA dataset, and Mitohelper’s 12S rRNA + SILVA v138 16S rRNA + SILVA v138 18S rRNA are available for download
Mitohelper and its reference datasets are updated approximately monthly and available at https://github.com/aomlomics/mitohelper. The paper describing Mitohelper is available here (DOI: 10.1002/edn3.187).