MitoFish, MitoAnnotator, and MiFish Pipeline: Updates in ten years.

MitoFish, MitoAnnotator, and MiFish Pipeline are a comprehensive database of fish mitochondrial genomes (mitogenomes), accurate annotation software of fish mitogenomes, and a web platform for metabarcoding analysis of fish mitochondrial environmental DNA (eDNA), respectively. The MitoFish Suite currently receives over 48,000 visits worldwide each year. Though, the performance and usefulness of the online platforms can still be improved. Here, we present essential updates on these platforms, including enrichment of the reference datasets, enhanced searching function, substantially faster genome annotation and eDNA analysis with the denoising of sequencing errors, and a multi-sample comparative analysis function. These updates have made our platform more intuitive, effective, and reliable. These updated platforms are freely available at http://mitofish.aori.u-tokyo.ac.jp/.