I am a beginner in bioinformatics and I am looking for a robust pipeline to identify optimal shRNA targets within a highly variable transposable element (TE) family. My idea is to aggregate public long-read sequencing data (e.g., PacBio) to pinpoint regions with the highest read coverage and the lowest sequence entropy relative to a consensus sequence. Could anyone suggest a workflow or specific tools to identify such windows of high coverage and high sequence conservation across multiple long-read datasets? Any guidance for someone with limited bioinformatics experience would be greatly appreciated.