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

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...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) England), 2023-01, Vol.39 (1)
Main Authors: Dishuck, Philip C, Rozanski, Allison N, Logsdon, Glennis A, Porubsky, David, Eichler, Evan E
Format: Article
Language:English
Subjects:
Applications Note
Assemblies
Assembly
Availability
Bioinformatics
Diploids
Gene sequencing
Genome
Genomes
High-Throughput Nucleotide Sequencing - methods
Humans
Nanopores
Sequence Analysis, DNA - methods
Software
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Summary: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.
ISSN:1367-4811
1367-4803
1367-4811
DOI:10.1093/bioinformatics/btac714