sequencing platforms (Oxford Nanopore)

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Oxford Nanopore sequencing platforms
An illustration of targeted amplicon and metagenomic <t>sequencing</t> approaches. A schematic overview demonstrating diverse sample types along with commonly utilized sequencing platforms, as well as systematic and stepwise data processing steps.

An illustration of targeted amplicon and metagenomic <t>sequencing</t> approaches. A schematic overview demonstrating diverse sample types along with commonly utilized sequencing platforms, as well as systematic and stepwise data processing steps.

Sequencing Platforms, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/sequencing+platforms/sequencing+platform/pmc07820839-171-12-9
Average 90 stars, based on 1 article reviews

sequencing platforms - by Bioz Stars, 2026-11

90/100 stars

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1) Product Images from "Current challenges and best-practice protocols for microbiome analysis"

Article Title: Current challenges and best-practice protocols for microbiome analysis

Journal: Briefings in Bioinformatics

doi: 10.1093/bib/bbz155

An illustration of targeted amplicon and metagenomic sequencing approaches. A schematic overview demonstrating diverse sample types along with commonly utilized sequencing platforms, as well as systematic and stepwise data processing steps.

Figure Legend Snippet: An illustration of targeted amplicon and metagenomic sequencing approaches. A schematic overview demonstrating diverse sample types along with commonly utilized sequencing platforms, as well as systematic and stepwise data processing steps.

Techniques Used: Amplification, Sequencing

A schematic overview outlining various experimental and computational challenges associated with 16S rRNA-based and shotgun metagenomic sequencing.

Figure Legend Snippet: A schematic overview outlining various experimental and computational challenges associated with 16S rRNA-based and shotgun metagenomic sequencing.

Techniques Used: Sequencing

Major short-read and long-read sequencing technologies. ( A ) Illumina sequencing involves initial trimming, adenylation of the blunt ends and ligation of specific adapters to DNA molecules. Following this library, fragments are amplified in situ on flow cell surfaces through bridge amplification and produce sequencing clusters. Finally, reversible dye terminator sequencing step is implemented where single-nucleotide addition reactions and presence of blocking group at the 3′-OH (of the ribose moiety) help to identify sequencing clusters through a reporter fluorescent signal. ( B ) PacBio sequencing involves a circular consensus sequencing (CCS) SMRTbell technique. Herein, ligation of hairpin adapters to each end of a duplex DNA molecule forms a closed loop, which is sequenced in a zero-mode waveguide (ZMW), fluorescence-based readout of nucleotide incorporation. Each strand in the duplex DNA is sequenced together in multiple passes, and the consensus sequences from both strands are incorporated. ( C ) Nanopore sequencing involves ligation of hairpin adapters at one end of duplex DNA molecule before initiating nanopore sequencing of the linked original DNA strands. The blockades in ionic current through the nanopore are optimally quantified as DNA base sequences.

Figure Legend Snippet: Major short-read and long-read sequencing technologies. ( A ) Illumina sequencing involves initial trimming, adenylation of the blunt ends and ligation of specific adapters to DNA molecules. Following this library, fragments are amplified in situ on flow cell surfaces through bridge amplification and produce sequencing clusters. Finally, reversible dye terminator sequencing step is implemented where single-nucleotide addition reactions and presence of blocking group at the 3′-OH (of the ribose moiety) help to identify sequencing clusters through a reporter fluorescent signal. ( B ) PacBio sequencing involves a circular consensus sequencing (CCS) SMRTbell technique. Herein, ligation of hairpin adapters to each end of a duplex DNA molecule forms a closed loop, which is sequenced in a zero-mode waveguide (ZMW), fluorescence-based readout of nucleotide incorporation. Each strand in the duplex DNA is sequenced together in multiple passes, and the consensus sequences from both strands are incorporated. ( C ) Nanopore sequencing involves ligation of hairpin adapters at one end of duplex DNA molecule before initiating nanopore sequencing of the linked original DNA strands. The blockades in ionic current through the nanopore are optimally quantified as DNA base sequences.

Techniques Used: Sequencing, Illumina Sequencing, Ligation, Amplification, In Situ, Blocking Assay, PacBio Sequencing, Fluorescence, Nanopore Sequencing

Best-practice protocol for the acquisition and analysis of targeted amplicon and shotgun metagenomics data from sequencing to functional annotation. The basic flow of experimental steps followed by downstream preprocessing and analysis steps is shown. At each step, the optimal tools utilized during the process are shown as well. All scripts are available at https://github.com/grimmlab/MicrobiomeBestPracticeReview .

Figure Legend Snippet: Best-practice protocol for the acquisition and analysis of targeted amplicon and shotgun metagenomics data from sequencing to functional annotation. The basic flow of experimental steps followed by downstream preprocessing and analysis steps is shown. At each step, the optimal tools utilized during the process are shown as well. All scripts are available at https://github.com/grimmlab/MicrobiomeBestPracticeReview .

Techniques Used: Amplification, Sequencing, Functional Assay

Sequencing:

Article Title: Pooled, long-read sequencing for structural variant characterization in schistosome populations.
Article Snippet: .. 30 31 Results 32 Sequencing Results – We generated long read data with Oxford Nanopore Technologies (ONT) 33 sequencing platform for five lab populations of S. mansoni; SmBRE, SmEG, SmOR and two 34 AC CE P ED M AN US CR IP T Downloaded from https://academ ic.oup.com /gbe/advance-article/doi/10.1093/gbe/evaf127/8176509 by guest on 28 June 2025 populations recently selected from a single population SmLE-PZQ-ER and SmLE-PZQ-ES (Table 1 1). ..

Article Title: Resolving RH and GYP hybrid alleles while accessing the entire blood group genome with Nanopore adaptive sampling
Article Snippet: .. This unique feature compatible with Oxford Nanopore Technologies (ONT) sequencing platforms enables enrichment of user-defined genomic regions though a computational approach , . ..

Article Title: Medlib: A Feature-Rich C/C++ Library for Exact Alignment of Nanopore Sequences Using Multiple Edit Distance
Article Snippet: .. However, the advent of long-read, high-error sequencing platforms—such as Oxford Nanopore Technologies—demands alignment tools that not only deliver exact results but also accommodate the elevated noise inherent in these data. ..

Article Title: Novel insights into the Leishmania infantum transcriptome diversity of protein-coding and non-coding sequences in both stages of parasite development using nanopore direct RNA sequencing.
Article Snippet: .. The Oxford Nanopore Technologies (ONT) sequencing platform was used to generate long reads of the L. infantum promastigote and amastigote-like transcriptomes. ..

Article Title: Restoring flowcell type and basecaller configuration from FASTQ files of nanopore sequencing data
Article Snippet: .. Specifically, this script first filtered the total SRA Runs based on two conditions: (1) the publication date of the SRA Run falls within the range of “2010/01/01” to “2024/01/09”; (2) the sequencing platform is Oxford Nanopore. ..

Article Title: A Systematic Review of the Advances and New Insights into Copy Number Variations in Plant Genomes.
Article Snippet: Currently, several commercial platforms use third-generation DNA sequencing technologies, such as Pacific Biosciences (PacBio) Single Molecule Real Time (SMRT) sequencing and Illumina’s TruSeq Synthetic Long-Read technology [53,54]. .. The representative of fourth-generation sequencing technology is the Oxford Nanopore sequencing platform [55]. ..

Generated:

PacBio Sequencing:

Article Title: GKNnet: an relational graph convolutional network-based method with knowledge-augmented activation layer for microbial structural variation detection.
Article Snippet: .. These datasets were obtained from the Oxford Nanopore and PacBio sequencing platforms, respectively. ..

Review