Some short-read analysis tools can be used with long-read data, especially if they include options optimized for longer read lengths. However, most short-read tools are built around assumptions that differ from long-read data, such as fixed read sizes, quality distributions, GC content, and the presence of native epigenetic signals.
For the most accurate and efficient results, it’s best to use tools specifically developed or configured for long-read sequencing data. Understanding the capabilities and limitations of your chosen software is key to achieving optimal outcomes.