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GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads
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 dev...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9805576/ https://www.ncbi.nlm.nih.gov/pubmed/36321867 http://dx.doi.org/10.1093/bioinformatics/btac714 |
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author | Dishuck, Philip C Rozanski, Allison N Logsdon, Glennis A Porubsky, David Eichler, Evan E |
author_facet | Dishuck, Philip C Rozanski, Allison N Logsdon, Glennis A Porubsky, David Eichler, Evan E |
author_sort | Dishuck, Philip C |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-9805576 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-98055762023-01-03 GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads Dishuck, Philip C Rozanski, Allison N Logsdon, Glennis A Porubsky, David Eichler, Evan E Bioinformatics Applications Note 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. Oxford University Press 2022-11-02 /pmc/articles/PMC9805576/ /pubmed/36321867 http://dx.doi.org/10.1093/bioinformatics/btac714 Text en © The Author(s) 2022. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Note Dishuck, Philip C Rozanski, Allison N Logsdon, Glennis A Porubsky, David Eichler, Evan E GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads |
title | GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads |
title_full | GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads |
title_fullStr | GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads |
title_full_unstemmed | GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads |
title_short | GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads |
title_sort | gavisunk: genome assembly validation via inter-sunk distances in oxford nanopore reads |
topic | Applications Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9805576/ https://www.ncbi.nlm.nih.gov/pubmed/36321867 http://dx.doi.org/10.1093/bioinformatics/btac714 |
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