GAVISUNK: Genome assembly validation via inter-SUNK distances in Oxford Nanopore reads

MotivationHighly contiguous de novo genome assemblies are now feasible for large numbers of species and individuals. Methods are needed to validate assembly accuracy and detect misassemblies with orthologous sequencing data to allow for confident downstream analyses. ResultsWe developed GAVISUNK, an open-source pipeline that detects misassemblies and produces a set of reliable regions genome-wide by assessing concordance of distances between unique k-mers in Pacific Biosciences high-fidelity (HiFi) assemblies and raw Oxford Nanopore Technologies reads. AvailabilityGAVISUNK is available at https://github.com/pdishuck/GAVISUNK. Contacteee@gs.washington.edu