GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads.
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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.
SUBMITTER: Dishuck PC
PROVIDER: S-EPMC9805576 | biostudies-literature | 2023 Jan
REPOSITORIES: biostudies-literature
Publications
GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads.
Dishuck Philip C PC Rozanski Allison N AN Logsdon Glennis A GA Porubsky David D Eichler Evan E EE
Bioinformatics (Oxford, England) 20230101 1
<h4>Motivation</h4>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.<h4>Results</h4>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 Pacif ...[more]
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