MitoFish, MitoAnnotator, and MiFish Pipeline: Updates in 10 Years

MitoFish, MitoAnnotator, and MiFish Pipeline are comprehensive databases 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 every year; however, the performance and usefulness of the online platforms can still be improved. Here, we present essential updates on these platforms, including an enrichment of the reference data sets, an enhanced searching function, substantially faster genome annotation and eDNA analysis with the denoising of sequencing errors, and a multisample comparative analysis function. These updates have made our platform more intuitive, effective, and reliable. These updated platforms are freely available at .

Automated summary

MitoFish, MitoAnnotator, and MiFish Pipeline are comprehensive databases and software for fish mitochondrial genomes, as well as a web platform for fish mitochondrial eDNA analysis. This article presents essential updates that have improved the performance and usefulness of these platforms, including enriched reference data sets, enhanced searching function, faster genome annotation and eDNA analysis with denoising of sequencing errors, and a new multisample comparative analysis function. These updates have made the platforms more intuitive, effective, and reliable. The updated platforms are freely available at .