« Home « Kết quả tìm kiếm

Nanopore sequencing

Tìm thấy 14+ kết quả cho từ khóa "Nanopore sequencing"

DNAscent v2: Detecting replication forks in nanopore sequencing data with deep learning

tailieu.vn

Detection of base analogs incorporated during DNA replication by nanopore sequencing. FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing

Whole-genome resequencing using nextgeneration and Nanopore sequencing for molecular characterization of T-DNA integration in transgenic poplar 741

tailieu.vn

Part of the flanking sequences were isolated from the junction reads obtained by NGS and the Sanger sequen- cing reads obtained from the PCR products. the other part of the flanking sequences and complete T-DNA se- quences were extracted from the junction reads obtained by genome resequencing using Nanopore sequencing..

Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing

tailieu.vn

Oxford Nanopore sequencing can generate long reads that span repetitive regions in bacterial genomes, thus resulting in less fragmented or even complete ge- nomes. Here, Oxford Nanopore long reads can scaffold contigs generated by Illumina short reads to disambiguate regions of the assembly graph that cannot be resolved by Illumina short reads alone, as implemented in assemblers such as MaSuRCA [8], SPAdes [9], and Unicycler [10]..

Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants

tailieu.vn

The compari- son of relative frequencies between the input and the nanopore output (actual versus reconstruction from nanopore sequencing) from both experiments showed that nanopore sequencing accurately reproduced the. Nanopore sequencing is cost effective for high throughput HCV sequencing. The nanopore sequencing run pro- duced on average 5141 reads per sample (range with a total output of 1.27 million reads (6.82Gbp total yield) during a run time of 47 h.

Promising prospects of nanopore sequencing for algal hologenomics and structural variation discovery

tailieu.vn

All Oxford nanopore platforms function on the basis of the same principle (and nanopore chemistries) for DNA sequencing, in which a single-stranded DNA (ssDNA) unfolding from a double stranded DNA (dsDNA) molecule threads through a nanopore embed- ded in a membrane to which voltage is applied.

Consistent ultra-long DNA sequencing with automated slow pipetting

tailieu.vn

By automating the slow pipetting of library preparation reagents, SNAILS increases the consistency and throughput of long read Nanopore sequencing.. Keywords: Oxford Nanopore technologies, GridION, MinION, DNA sequencing, Long read sequencing, Ultra-long, Ultra-high molecular weight DNA, de novo assembly. Illumina reads aligned to GRCh38 better than other long read sequencing technologies [4].

Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing

tailieu.vn

We would like to thank the DNA Sequencing Section and the Scientific Computing and Data Analysis Section of the Research Support Division at OIST for their support, Danny Miller for advices on Nanopore sequencing, Dan Rokhsar, Gene Myers, Ferdinand Marlétaz and Konstantin Khalturin for critical comments, Takeshi Onuma and Hiroki Nishida for sharing the OSKA2016 genome sequence prior publication, Simon Henriet for the technical advice on the DNA extraction protocol, and Lin Zhang for helping with

Comparison of the performance of an amplicon sequencing assay based on Oxford Nanopore technology to real-time PCR assays for detecting bacterial biodefense pathogens

tailieu.vn

Conclusions: Based on these results, we propose amplicon sequencing assay as a viable alternative to replace the current real-time PCR based singleplex assays for higher throughput biodefense applications. Keywords: Biodefense, Biodetection, Biosurveillance, Oxford Nanopore sequencing, Real-time PCR, High throughput PCR assay, LoD, Singleplex, Multiplex.

Re-examination of two diatom reference genomes using long-read sequencing

tailieu.vn

Long-read sequencing has the potential to give rise to highly contiguous scaffolds representing all or most of an organism’s chromosomes (see e.g., the recent Nanopore sequencing of the model nematode C. We view our long-read assemblies as additional genomic datasets that do not replace but complement and enhance the existing Sanger-based reference genomes – in isolation, neither provides a complete picture of the P.

A new method for long-read sequencing of animal mitochondrial genomes: Application to the identification of equine mitochondrial DNA variants

tailieu.vn

Complete mitochondrial genome of the green-lipped mussel, Perna canaliculus (Mollusca: Mytiloidea), from long nanopore sequencing reads.. Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication.

The symbiotic relationship between Caenorhabditis elegans and members of its microbiome contributes to worm fitness and lifespan extension

tailieu.vn

L4-young adult worms grown with the bacteria of interest were subjected to RNAseq, followed by nanopore sequencing of the ge- nomes of these bacteria. Finally, the effect of the metab- olite of interest (vitamin B6) was tested on worm lifespan..

Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

tailieu.vn

In contrast, the long reads generated by nanopore sequencing platforms can resolve many of the genomic and intergenomic repeats.. and a second work which validated the bioinformatic SNP and cgMLST source tracking efficiency of the quasimetagenomic data [26];.

Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies

tailieu.vn

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution.. The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. of the European eel genome from nanopore sequencing reads. First draft genome sequence of the Japanese eel, Anguilla japonica. Draft genome of the American eel (Anguilla rostrata). Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes.

The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation

tailieu.vn

It can be envisioned that the completeness of lncRNAs will be remarkably improved with the application of PacBio SMRT or Nanopore sequencing strategies [32, 33]. Additionally, the num- bers of lncRNAs reported in various insects varied greatly, this might be caused by multiple factors, such as sequencing depth, different analysis approaches, and parameter settings.. In this study, the characteristics of lncRNAs were re- vealed through comparison with mRNAs.

Yes, we can use it: A formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics and barcoding research using the Caribbean spiny lobster Panulirus argus

tailieu.vn

Nanopore sequencing and assembly of a human genome with ultra-long-read. Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication. Two reads to rule them all: Nanopore long read-guided assembly of the iconic Christmas Island red crab, Gecarcoidea natalis (Pocock, 1888), mitochondrial genome and the challenges of AT-rich mitogenomes.

Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors

tailieu.vn

Nanopore sequencing reads for BioProject PRJNA625113 have been deposited in the NCBI SRA under accession number SRR11536473 for C5. https://doi.org . https://doi.org/10.1094/Phyto-62-729.. https://doi.org/1 0.1094/Phyto-71-1073.. https://doi.org/10.1094/PD- 90-0989.. https://doi.org/10.1126/. https://doi.. org/10.1094/Phyto-73-585..

Improving protein domain classification for third-generation sequencing reads using deep learning

tailieu.vn

Resolving the complexity of the human genome using single-molecule sequencing

Complete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read sequencing

tailieu.vn

Long-read sequencing promises an enhanced ability to complete bacterial genomes. The most commonly avail- able techniques for long-read sequencing are the Single Molecule Real-Time (SMRT) technology by Pacific Bio- sciences® (PacBio, United States) and the newer Oxford Nanopore Technologies (ONT, United Kingdom) MinION .

Completion of draft bacterial genomes by long-read sequencing of synthetic genomic pools

tailieu.vn

However, despite efforts to improve the accuracy of long-read de novo as- sembly algorithms [22–25], the high error rate of reads generated by PacBio and Oxford Nanopore platforms can result in the introduction of assembly errors [13]. In addition, the high per-genome cost of library prepar- ation, particularly for multiplexed PacBio sequencing, is a limiting factor for widespread application of long-read.

Whole genome sequencing of Borrelia miyamotoi isolate Izh-4: Reference for a complex bacterial genome

tailieu.vn

Results: We used multiple available sequencing methods, including Pacific Bioscience single-molecule real-time technology (SMRT) and Oxford Nanopore technology (ONT) supplemented with highly accurate Illumina sequences, to explore the suitability for whole genome assembly of the Russian B.