Rapid mitochondrial genome sequencing based on Oxford Nanopore Sequencing and a proxy for vertebrate species identification
Sign Up to like & getrecommendations! Published in 2020 at "Ecology and Evolution"
DOI: 10.1002/ece3.6151
Abstract: Abstract Molecular information is crucial for species identification when facing challenging morphology‐based specimen identifications. The use of DNA barcodes partially solves this problem, but in some cases when PCR is not an option (i.e., primers… read more here.
Keywords: species identification; rapid mitochondrial; mitochondrial genome; genome ... See more keywords
Polishing the Oxford Nanopore long-read assemblies of bacterial pathogens with Illumina short reads to improve genomic analyses.
Sign Up to like & getrecommendations! Published in 2021 at "Genomics"
DOI: 10.1016/j.ygeno.2021.03.018
Abstract: Oxford Nanopore sequencing has been widely used to achieve complete genomes of bacterial pathogens. However, the error rates of Oxford Nanopore long reads are high. Various polishing algorithms using Illumina short reads to correct the… read more here.
Keywords: illumina short; short reads; real reads; nanopore long ... See more keywords
Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data
Sign Up to like & getrecommendations! Published in 2022 at "Nature Communications"
DOI: 10.1038/s41467-022-28852-1
Abstract: Infectious disease monitoring on Oxford Nanopore Technologies (ONT) platforms offers rapid turnaround times and low cost. Tracking low frequency intra-host variants provides important insights with respect to elucidating within-host viral population dynamics and transmission. However,… read more here.
Keywords: oxford nanopore; host viral; intra host; frequency ... See more keywords
Prowler: A novel trimming algorithm for Oxford Nanopore sequence data.
Sign Up to like & getrecommendations! Published in 2021 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btab630
Abstract: MOTIVATION Trimming and filtering tools are useful in DNA sequencing analysis because they increase the accuracy of sequence alignments and thus the reliability of results. Oxford Nanopore Technologies (ONT) trimming and filtering tools are currently… read more here.
Keywords: prowler novel; prowler; novel trimming; trimming algorithm ... See more keywords
GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac714
Abstract: 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… read more here.
Keywords: genome assembly; oxford nanopore; validation via; gavisunk genome ... See more keywords
Nanocall: an open source basecaller for Oxford Nanopore sequencing data
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btw569
Abstract: Motivation: The highly portable Oxford Nanopore MinION sequencer has enabled new applications of genome sequencing directly in the field. However, the MinION currently relies on a cloud computing platform, Metrichor (metrichor.com), for translating locally generated… read more here.
Keywords: sequencing data; nanopore sequencing; open source; oxford nanopore ... See more keywords
Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American Fundulus killifish
Sign Up to like & getrecommendations! Published in 2020 at "GigaScience"
DOI: 10.1093/gigascience/giaa067
Abstract: Abstract Background Whole-genome sequencing data from wild-caught individuals of closely related North American killifish species (Fundulus xenicus, Fundulus catenatus, Fundulus nottii, and Fundulus olivaceus) were obtained using long-read Oxford Nanopore Technology (ONT) PromethION and short-read… read more here.
Keywords: nanopore technology; draft; illumina; north american ... See more keywords
The use of Oxford Nanopore native barcoding for complete genome assembly
Sign Up to like & getrecommendations! Published in 2017 at "GigaScience"
DOI: 10.1093/gigascience/gix001
Abstract: Abstract Background The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using… read more here.
Keywords: short read; native barcoding; read data; genome ... See more keywords
De novo assembly of the Indian blue peacock (Pavo cristatus) genome using Oxford Nanopore technology and Illumina sequencing
Sign Up to like & getrecommendations! Published in 2019 at "GigaScience"
DOI: 10.1093/gigascience/giz038
Abstract: Abstract Background The Indian peafowl (Pavo cristanus) is native to South Asia and is the national bird of India. Here we present a draft genome sequence of the male blue peacock using Illumina and Oxford… read more here.
Keywords: nanopore technology; novo assembly; genome; peacock ... See more keywords
Optimized use of Oxford Nanopore flowcells for hybrid assemblies
Sign Up to like & getrecommendations! Published in 2020 at "Microbial Genomics"
DOI: 10.1099/mgen.0.000453
Abstract: Hybrid assemblies are highly valuable for studies of Enterobacteriaceae due to their ability to fully resolve the structure of mobile genetic elements, such as plasmids, which are involved in the carriage of clinically important genes… read more here.
Keywords: use oxford; nanopore flowcells; running times; optimized use ... See more keywords
Recovery of small plasmid sequences via Oxford Nanopore sequencing.
Sign Up to like & getrecommendations! Published in 2021 at "Microbial genomics"
DOI: 10.1099/mgen.0.000631
Abstract: Oxford Nanopore Technologies (ONT) sequencing platforms currently offer two approaches to whole-genome native-DNA library preparation: ligation and rapid. In this study, we compared these two approaches for bacterial whole-genome sequencing, with a specific aim of… read more here.
Keywords: read sets; ligation; plasmid sequences; oxford nanopore ... See more keywords