Protocol for accurately annotating circular RNA and microRNA in giant vertebrate genomes

With the advent of long-read sequencing techniques, there has been an increase in the sequencing and assembly of giant genomes such as salamanders and lungfish. Here, I present a protocol for accurately annotating non-coding RNAs, specifically circular RNAs and microRNAs, using genomic and transcriptomic data. I describe quality checks and post hoc steps to minimize false-positive predictions in repeat element-rich genomes. This protocol has potential application for annotating non-coding RNAs in other giant vertebrate genomes. For complete details on the use and execution of this protocol, please refer to Brown et al.¹.