Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article 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.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9805576 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btac714 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
sp. nov. and sp. nov., isolated from forest soil in Ireland.
Int J Syst Evol Microbiol
September 2025
School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
Two yeast strains, PYCC 10015 and PYCC 10016, were isolated from soil from an Irish forest. Sequence analysis of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) of the rRNA gene repeat, and the D1/D2 domain of the LSU rRNA gene, showed that they belong to the and genera of the order , but they did not exactly match any known species.
View Article and Find Full Text PDFNext Generation Sequencing Improves Diagnostic 16S rRNA Amplicon-Based Microbiota Analyses of Clinical Samples Compared to Sanger Sequencing.
APMIS
September 2025
The Regional Department of Clinical Microbiology, Zealand University Hospital-Koege, Køge, Denmark.
Sequencing of the 16S ribosomal RNA (rRNA) gene is an important tool in addition to conventional methods for the identification of bacterial pathogens in human infections. In polymicrobial samples, Sanger sequencing can produce uninterpretable chromatograms. This limitation can be overcome by Next Generation Sequencing (NGS) of the 16S rRNA gene.
View Article and Find Full Text PDFPerformance of Rapid Clonotyping of Chronic Lymphocytic Leukemia Using Flongle Flow-Cell Nanopore Sequencing of IGH Rearrangements.
Eur J Haematol
September 2025
Haematology-Pathology Research Laboratory, Research Unit for Haematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark.
Background: Clonotyping of immunoglobulin heavy chain (IGH) gene rearrangements is critical for diagnosis, prognostication, and measurable residual disease monitoring in chronic lymphocytic leukemia (CLL). Although short-read next-generation sequencing (NGS) platforms, such as Illumina MiSeq, are widely used, they face challenges in spanning full VDJ rearrangements. Long-read sequencing via Oxford Nanopore Technologies (ONT) offers a potential alternative using the compact and cost-effective flow cells.
View Article and Find Full Text PDFGenomic and metabolomic insights into the biosynthesis of carotenoids and lipids in oleaginous red yeast Cystofilobasidium infirmominiatum HZR20 isolated from Mangrove plants in Southern China.
Arch Microbiol
September 2025
College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China.
Cystofilobasidium infirmominiatum, biotechnologically significant yeast, is increasingly garnering attention due to its superior ability to produce valuable carotenoids and lipids. Nonetheless, until now, the reference genome that governs the biosynthesis of carotenoids and lipids in C. infirmominiatum remains unreported.
View Article and Find Full Text PDFA cross-disciplinary hands-on genomics curriculum adaptable for high school to undergraduate education.
J Microbiol Biol Educ
September 2025
University of California Riverside, Riverside, California, USA.
DNA literacy is becoming increasingly essential for navigating healthcare, understanding pandemics, and engaging with biotechnology-yet genomics education remains limited at the secondary level of education. We present a modular, hands-on curriculum designed for high school and early undergraduate students (ages 14-21) that introduces key genomics concepts through an experiment on fermentation, a process that is key to food preservation and medicine. Students follow a complete scientific process: exploring what DNA is and how microbial succession works, analyzing real DNA sequencing data, and writing a formal scientific report.
View Article and Find Full Text PDF