rMETL: sensitive and fast mobile element insertion detection with long read realignment

Abstract

SummaryMobile element insertion (MEI) is a major category of structure variations (SVs). The rapid development of long read sequencing provides the opportunity to sensitively discover MEIs. However, the signals of MEIs implied by noisy long reads are highly complex, due to the repetitiveness of mobile elements as well as the serious sequencing errors. Herein, we propose Realignment-based Mobile Element insertion detection Tool for Long read (rMETL). rMETL takes advantage of its novel chimeric read re-alignment approach to well handle complex MEI signals. Benchmarking results on simulated and real datasets demonstrated that rMETL has the ability to more sensitivity discover MEIs as well as prevent false positives. It is suited to produce high quality MEI callsets in many genomics studies.\n\nAvailability and Implementation: rMETL is available from https://github.com/hitbc/rMETL.\n\nContact: ydwang@hit.edu.cn\n\nSupplementary information: Supplementary data are available at Bioinformatics online.