Yanosim has three options:

1. yanosim model: Creates an model of mismatches, insertions and deletions based on an alignment of nanopore DRS reads to a reference. Reads should be aligned to a transcriptome i.e. without spliced alignment, using minimap2. They should have the cs tag. 2. yanosim quantify: Quantify the number of reads mapping to each transcript in a reference, so that the right number of reads can be simulated. 3. yanosim simulate: Given a model created using yanosim model, and per-transcript read counts created using yanosim simulate, simulate error-prone long-reads from the given fasta file.