Abstract
Motivation
Highly contiguous de novo phased diploid 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.
Results
We 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 assemblies and raw Oxford Nanopore Technologies reads.
Availability and implementation
GAVISUNK is available at https://github.com/pdishuck/GAVISUNK.
Supplementary information
Supplementary data are available at Bioinformatics online.
© The Author(s) 2022. Published by Oxford University Press.
2022
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
