Benchmarking tools for DNA repeat identification in diverse genomes

Abstract

Continuous progression in genomics shows that repeats are important elements of genomes that perform many regulatory and other functions. Eventually, to date, many computational tools have been developed and frequently used for the identification and analysis of genomic repeats. A single tool cannot detect all different types of repeats in diverse species rather pipeline of tools is more effective. But, the choice of such rigorous and robust tools is highly challenging. A method has been implemented to select a set of optimal tools for finding all available classes of perfect and imperfect tandem repeats including microsatellites, minisatellites, and interspersed CRISPRs in genomes. A total of 11 tools have been shortlisted using rule-based selection and then ranked by analyzing rigorousness in searching in diverse species and execution time. Tool comparison shows consistency in perfect microsatellite detection performance but significantly differ for long and imperfect repeats. A web-server has been built which provides a generic platform for various classes of repeat identification from the diverse genome using multiple tools and comparison.