ArticleBioinformatics (Oxford, England)2023
GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
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- mm2-ivh: simple and precise overlap detection in alpha satellite HORs with interval hashing.Bioinformatics (Oxford, England) · 2026Article
- A global view of human centromere variation and evolution.bioRxiv : the preprint server for biology · 2025Article
- Structural variation, selection, and diversification of the NPIP gene family from the human pangenome.Cell genomics · 2025Article
- Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs.Molecular ecology resources · 2025Article
- Independent expansion, selection, and hypervariability of theGenome research · 2024Article
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- Independent expansion, selection and hypervariability of thebioRxiv : the preprint server for biology · 2024Article
- The variation and evolution of complete human centromeres.bioRxiv : the preprint server for biology · 2023Article
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Authors and funding
5 authors.
Funding
Abstract
motivationHighly 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.
resultsWe 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.
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