Skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements.

ABSTRACT: Motivation: Mobile genetic elements (MGEs) are as ubiquitous in nature as they are varied in type, ranging from viral insertions to transposons to incorporated plasmids. Horizontal transfer of MGEs across bacterial species may also pose a significant threat to global health due to their capability to harbor antibiotic resistance genes. However, despite cheap and rapid whole-genome sequencing, the varied nature of MGEs makes it difficult to fully characterize them, and existing methods for detecting MGEs often do not agree on what should count. In this manuscript, we first define and argue in favor of a divergence-based characterization of mobile-genetic elements. Results: Using that paradigm, we present skandiver, a tool designed to efficiently detect MGEs from whole-genome assemblies with

SUBMITTER: Zhang XB 

PROVIDER: S-EPMC11373320 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature