Can I use my short-read sequencing software to analyze long-read sequencing data?

The underlying algorithms for many tools assume certain read length characteristics (set short read sizes vs variable lengths of long reads), quality distributions, data characteristics (GC content, native epigentics), etc… that will differ between short reads and long reads. Some tools originally developed for short reads also have run options optimized for long reads. Therefore, it is important to understand the tool. In general, it is recommended when analyzing long reads to use a tool developed for long reads or with options tailored for long reads to get an optimal results.