Related Experiment Video
Updated: Aug 1, 2026

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
Published on: June 23, 2012
GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads
Philip C Dishuck1, Allison N Rozanski1, Glennis A Logsdon1
1Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
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.
Related Concept Videos
Sanger Sequencing
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Genome Annotation and Assembly

