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

Motivation: Highly 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. Results: We developed GAVISUNK...

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Bibliographic Details
Published inbioRxiv
Main Authors Dishuck, Philip C, Rozanski, Allison N, Logsdon, Glennis A, Eichler, Evan E
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 18.06.2022
Subjects
Genomes
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Summary:Motivation: Highly 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. 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 (HiFi) assemblies and raw Oxford Nanopore Technologies reads. Competing Interest Statement E.E.E. is a scientific advisory board (SAB) member of Variant Bio, Inc.
DOI:10.1101/2022.06.17.496619