SatXplor – A comprehensive pipeline for satellite DNA analyses in complex genome assemblies

Abstract Satellite DNAs (satDNAs) are tandemly repeated sequences that make up a significant portion of almost all eukaryotic genomes. Although satDNAs have been shown to play a very important role in genome organization and evolution, they are relatively poorly analysed even in model. One of the main reasons for the current lack of in-depth studies on satDNAs is their underrepresentation in genome assemblies. The complexity and highly repetitive nature of satDNAs make their analysis challenging, and there is a need for efficient tools that can ensure accurate annotation and analysis of satDNAs. We present a novel pipeline, named Satellite DNA Exploration (SatXplor), designed to robustly characterize satDNA elements and analyse their arrays and flanking regions. SatXplor is benchmarked against curated satDNA datasets from diverse species, showcasing its versatility across genomes with varying complexities and different satDNA profile. Component algorithms excel in the identification of tandemly repeated sequences and for the first time enable evaluation of satDNA variation and array annotation with the addition of information about surrounding genomic landscape. SatXplor is an innovative pipeline for satDNA analysis that can be paired with any tool used for satDNA detection, offering insights into the structural characteristics, array determination and genomic context of satDNA elements. By integrating various computational techniques, from sequence analysis and homology investigation to advanced clustering and graph-based methods, it provides a versatile and comprehensive approach to explore the complexity of satDNA organization and to understand the underlying mechanisms and evolutionary aspects. It is open-source and freely accessible at https://github.com/mvolar/SatXplor .