scholarly journals NanoSim: nanopore sequence read simulator based on statistical characterization

2016 ◽  
Author(s):  
Chen Yang ◽  
Justin Chu ◽  
Ren&eacute L Warren ◽  
Inanç Birol
Keyword(s):  
Single Molecule ◽  
Sequencing Technology ◽  
Statistical Characterization ◽  
Single Molecule Sequencing ◽  
Sequencing Platform ◽  
Early Access ◽  
Oxford Nanopore ◽  
Commercial Technology ◽  
Read Simulator ◽  
Oxford Nanopore Technologies

Motivation: In 2014, Oxford Nanopore Technologies (ONT) announced a new sequencing platform called MinION. The particular features of MinION reads, longer read lengths and single-molecule sequencing in particular, show potential for genome characterization. As of yet, the pre-commercial technology is exclusively available through early-access, and only a few datasets are publically available for testing. Further, no software exists that simulates MinION platform reads with genuine ONT characteristics. Results: In this article, we introduce NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology. Availability: NanoSim is written in Python and R. The source files and manual are available at the Genome Sciences Centre website: http://www.bcgsc.ca/platform/bioinfo/software/nanosim

scholarly journals Prospects for the use of third generation sequencers for quantitative profiling of transcriptome

2018 ◽  
Vol 1 (4) ◽  
pp. e00086
Author(s):  
S.P. Radko ◽  
L.K. Kurbatov ◽  
K.G. Ptitsyn ◽  
Y.Y. Kiseleva ◽  
E.A. Ponomarenko ◽  
...  
Keyword(s):  
Single Molecule ◽  
Transcriptome Profiling ◽  
Third Generation ◽  
Sequencing Technology ◽  
Single Molecule Sequencing ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Biotechnology Companies ◽  
Oxford Nanopore Technologies ◽  
Quantitative Profiling

Transcriptome profiling is widely employed to analyze transcriptome dynamics when studying various biological processes at the cell and tissue levels. Unlike the second generation sequencers, which sequence relatively short fragments of nucleic acids, the third generation DNA/RNA sequencers developed by biotechnology companies “PacBio” and “Oxford Nanopore Technologies” allow one to sequence transcripts as single molecules and may be considered as potential molecular counters capable to measure the number of copies of each transcript with high throughput, sensitivity, and specificity. In the present review, the features of single molecule sequencing technologies offered by “PacBio” and “Oxford Nanopore Technologies” are considered alongside with their utility for transcriptome analysis, including the analysis of transcript isoforms. The prospects and limitations of the single molecule sequencing technology in application to quantitative transcriptome profiling are also discussed.

scholarly journals Assessing the quality of Astragalus fermented using Lactobacillus plantarum and Enterococcus faecium by its physicochemical properties and monitoring the bacterial composition with single molecule, real-time sequencing technology

2018 ◽  
Author(s):  
Hongxing Qiao ◽  
Xiaojing Zhang ◽  
Hongtao Shi ◽  
Yuzhen Song ◽  
Chuanzhou Bian
Keyword(s):  
Real Time ◽  
Lactobacillus Plantarum ◽  
Single Molecule ◽  
Enterococcus Faecium ◽  
Sequencing Technology ◽  
Production Rates ◽  
Microbial Composition ◽  
Sequencing Platform ◽  
Positive Effects

Background. Astragalus was a well-known traditional herbal medicine, widely used in human s , livestock and poultry in China and E ast Asia. Fermentation could improve health-promoting biological substance by probiotics. Methods. We investigated Astragalus that was fermented using probiotics including Enterococcus faecium , Lactobacillus plantarum and E nterococcus faecium + L actobacillus plantarum and applied the PacBio single molecule, real-time sequencing technology (SMRT) to evaluat e the quality of Astragalus fermentation production. Results. We found the production rates of acetic acid, methylacetic acid , ethylacetic acid and lactic acid using E. faecium + L. plantarum fermentation were 1866.24 mg/kg on day 15 , 203.80 mg/kg on day 30 , 996.04 mg/kg on day 15 and 3081.99 mg/kg on day 20 , respectively. Other production rates were: polysaccharide s, 9.43%, 8.51% and 7 . 59% on day 10; saponins , 19.6912 mg/g, 21.6630 mg/g and 20.2084 mg/g on day 15; and flavonoid s, 1.9032 mg/g, 2.0835 mg/g and 1.7086 mg/g on day 20 using E . faecium , L . plantarum and E. faecium + L. plantarum , respectively. According to SMRT analysis of the microbial composition s of nine Astragalus samples, we found after fermentation on day 3 , E. faecium and L. plantarum became the most prevalent species. Moreover, E. faecium + L. plantarum gave more positive effects than single strains in the Astragalus solid state fermentation process. Inclusion. Our data have demonstrate d that the SMRT sequencing platform is applicable to assessing the quality of Astragalus fermentation.

scholarly journals Parallel and scalable workflow for the analysis of Oxford Nanopore direct RNA sequencing datasets

2019 ◽  
Author(s):  
Luca Cozzuto ◽  
Huanle Liu ◽  
Leszek P. Pryszcz ◽  
Toni Hermoso Pulido ◽  
Julia Ponomarenko ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Single Molecule ◽  
Tail Length ◽  
Rna Modification ◽  
Sequencing Data ◽  
Polya Tail ◽  
Sequencing Platform ◽  
Rna Molecules ◽  
Oxford Nanopore ◽  
Quality Filtering

ABSTRACTThe direct RNA sequencing platform offered by Oxford Nanopore Technologies allows for direct measurement of RNA molecules without the need of conversion to complementary DNA, fragmentation or amplification. As such, it is virtually capable of detecting any given RNA modification present in the molecule that is being sequenced, as well as provide polyA tail length estimations at the level of individual RNA molecules. Although this technology has been publicly available since 2017, the complexity of the raw Nanopore data, together with the lack of systematic and reproducible pipelines, have greatly hindered the access of this technology to the general user. Here we address this problem by providing a fully benchmarked workflow for the analysis of direct RNA sequencing reads, termed MasterOfPores. The pipeline converts raw current intensities into multiple types of processed data, providing metrics of the quality of the run, quality-filtering, base-calling and mapping. The output of the pipeline can in turn be used to compute per-gene counts, RNA modifications, and prediction of polyA tail length and RNA isoforms. The software is written using the NextFlow framework for parallelization and portability, and relies on Linux containers such as Docker and Singularity for achieving better reproducibility. The MasterOfPores workflow can be executed on any Unix-compatible OS on a computer, cluster or cloud without the need of installing any additional software or dependencies, and is freely available in Github (https://github.com/biocorecrg/master_of_pores). This workflow will significantly simplify the analysis of nanopore direct RNA sequencing data by non-bioinformatics experts, thus boosting the understanding of the (epi)transcriptome with single molecule resolution.

scholarly journals Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

2018 ◽  
Author(s):  
Ruibang Luo ◽  
Fritz J. Sedlazeck ◽  
Tak-Wah Lam ◽  
Michael C. Schatz
Keyword(s):  
Neural Network ◽  
Single Molecule ◽  
Variant Calling ◽  
Accurate Identification ◽  
Whole Genome Analysis ◽  
Single Molecule Sequencing ◽  
Oxford Nanopore ◽  
Indel Length ◽  
Human Sample ◽  
Dna Sequence Variants

AbstractThe accurate identification of DNA sequence variants is an important, but challenging task in genomics. It is particularly difficult for single molecule sequencing, which has a per-nucleotide error rate of ~5%-15%. Meeting this demand, we developed Clairvoyante, a multi-task five-layer convolutional neural network model for predicting variant type (SNP or indel), zygosity, alternative allele and indel length from aligned reads. For the well-characterized NA12878 human sample, Clairvoyante achieved 99.73%, 97.68% and 95.36% precision on known variants, and 98.65%, 92.57%, 87.26% F1-score for whole-genome analysis, using Illumina, PacBio, and Oxford Nanopore data, respectively. Training on a second human sample shows Clairvoyante is sample agnostic and finds variants in less than two hours on a standard server. Furthermore, we identified 3,135 variants that are missed using Illumina but supported independently by both PacBio and Oxford Nanopore reads. Clairvoyante is available open-source (https://github.com/aquaskyline/Clairvoyante), with modules to train, utilize and visualize the model.

scholarly journals Ready-to-use nanopore platform for the detection of any DNA/RNA oligo at attomole range using an Osmium tagged complementary probe

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Albert S. W. Kang ◽  
Janette G. Bernasconi ◽  
William Jack ◽  
Anastassia Kanavarioti
Keyword(s):  
Single Molecule ◽  
Point Of Care ◽  
Complex Mixture ◽  
Channel Measurements ◽  
Single Digit ◽  
Acquisition Rate ◽  
Oxford Nanopore ◽  
Strong Hybridization ◽  
Technology Probes ◽  
Oxford Nanopore Technologies

AbstractNanopores can serve as single molecule sensors. We exploited the MinION, a portable nanopore device from Oxford Nanopore Technologies, and repurposed it to detect any DNA/RNA oligo (target) in a complex mixture by conducting voltage-driven ion-channel measurements. The detection and quantitation of the target is enabled by the use of a unique complementary probe. Using a validated labeling technology, probes are tagged with a bulky Osmium tag (Osmium tetroxide 2,2′-bipyridine), in a way that preserves strong hybridization between probe and target. Intact oligos traverse the MinION’s nanopore relatively quickly compared to the device’s acquisition rate, and exhibit count of events comparable to the baseline. Counts are reported by a publicly available software, OsBp_detect. Due to the presence of the bulky Osmium tag, probes traverse more slowly, produce multiple counts over the baseline, and are even detected at single digit attomole (amole) range. In the presence of the target the probe is “silenced”. Silencing is attributed to a 1:1 double stranded (ds) complex that does not fit and cannot traverse this nanopore. This ready-to-use platform can be tailored as a diagnostic test to meet the requirements for point-of-care cell-free tumor DNA (ctDNA) and microRNA (miRNA) detection and quantitation in body fluids.

Nanotrap Particles Improve Nanopore Sequencing of SARS-CoV-2 and Other Respiratory Viruses

2021 ◽  
Author(s):  
Patrick Daniel Andersen ◽  
Stephanie Barksdale ◽  
Robert Alex Barclay ◽  
Natalie Smith ◽  
Justin Fernandes ◽  
...  
Keyword(s):  
Rna Extraction ◽  
Nanopore Sequencing ◽  
Sequencing Platform ◽  
Magnetic Hydrogel ◽  
Oxford Nanopore ◽  
Input Sample ◽  
Lower Titer ◽  
Syncytial Virus ◽  
Hydrogel Particle ◽  
Oxford Nanopore Technologies

Presented here is a magnetic hydrogel particle enabled workflow for capturing and concentrating SARS-CoV-2 from diagnostic remnant swab samples that significantly improves sequencing results using the Oxford Nanopore Technologies MinION sequencing platform. Our approach utilizes a novel affinity-based magnetic hydrogel particle, circumventing low input sample volumes and allowing for both rapid manual and automated high throughput workflows that are compatible with nanopore sequencing. This approach enhances standard RNA extraction protocols, providing up to 40x improvements in viral mapped reads, and improves sequencing coverage by 20-80% from lower titer diagnostic remnant samples. Furthermore, we demonstrate that this approach works for contrived influenza virus and respiratory syncytial virus samples, suggesting that it can be used to identify and improve sequencing results of multiple viruses in VTM samples. These methods can be performed manually or on a KingFisher Apex system.

scholarly journals Early MinION™ nanopore single-molecule sequencing technology enables the characterization of hepatitis B virus genetic complexity in clinical samples

PLoS ONE ◽  
2018 ◽  
Vol 13 (3) ◽  
pp. e0194366 ◽  
Author(s):  
Virginie Sauvage ◽  
Laure Boizeau ◽  
Daniel Candotti ◽  
Mathias Vandenbogaert ◽  
Annabelle Servant-Delmas ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Single Molecule ◽  
Clinical Samples ◽  
Sequencing Technology ◽  
Single Molecule Sequencing ◽  
Genetic Complexity ◽  
B Virus

scholarly journals Genetic Adaptation of Porcine Circovirus Type 1 to Cultured Porcine Kidney Cells Revealed by Single-Molecule Long-Read Sequencing Technology

2017 ◽  
Vol 5 (5) ◽  
Author(s):  
Dóra Tombácz ◽  
Norbert Moldován ◽  
Zsolt Balázs ◽  
Zsolt Csabai ◽  
Michael Snyder ◽  
...  
Keyword(s):  
Single Molecule ◽  
Porcine Circovirus Type ◽  
Porcine Circovirus ◽  
Genetic Adaptation ◽  
Kidney Cells ◽  
Porcine Kidney ◽  
Sequencing Technology ◽  
Sequencing Platform ◽  
Long Read

ABSTRACT Porcine circovirus type 1 (PCV1) is a nonpathogenic circovirus, and a contaminant of the porcine kidney (PK-15) cell line. We present the complete and annotated genome sequence of strain Szeged of PCV1, determined by Pacific Biosciences RSII long-read sequencing platform.

scholarly journals Application of monomolecular sequencing technology to the diagnostics of hypertrophic cardiomyopathy

2020 ◽  
pp. 9-10
Author(s):  
Р.Р. Салахов ◽  
М.В. Голубенко ◽  
Е.Н. Павлюкова ◽  
А.В. Марков ◽  
Н.П. Бабушкина ◽  
...  
Keyword(s):  
Data Analysis ◽  
Hypertrophic Cardiomyopathy ◽  
Sequencing Technology ◽  
Missense Variants ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

В работе представлены результаты секвенирования пяти генов, ассоциированных с гипертрофической кардиомиопатией, с использованием технологии мономолекулярного секвенирования компании Oxford Nanopore Technologies. В результате анализа данных с помощью различных алгоритмов были выявлены миссенс-варианты в исследованных генах, которые могут являться причиной заболевания у пациентов. The paper presents the results of sequencing of five genes associated with hypertrophic cardiomyopathy, using monomolecular sequencing (Oxford Nanopore Technologies). As a result of data analysis with various algorithms, missense variants were identified in the studied genes that may be the cause of the disease in the patients.

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