A Statistical Analysis of Duplication Errors in the Nanopore Sequencing Channel

A duplication edit, which copies a substring and inserts the copy immediately after the substring itself, is a type of error in communication systems and DNA storage. In this work, we devise an algorithm for computing the duplication distance, i.e., the minimum cost of transforming one string to another using insertions, deletions, substitutions, duplications and deduplications, where each operation is assigned a weight determining its contribution to the cost. With the help of this algorithm, we perform a statistical analysis of simulated Nanopore data to determine whether duplication and deduplication edits are prevalent in the Nanopore sequencing channel. Our results indicate a positive answer to this question.