scholarly journals Real-time analysis for Nanopore sequencing data

2019 ◽  
Author(s):  
Hoang Son Nguyen
Keyword(s):  
Real Time ◽  
Nanopore Sequencing ◽  
Sequencing Data ◽  
Time Analysis ◽  
Real Time Analysis

scholarly journals Real-time monitoring and analysis of SARS-CoV-2 nanopore sequencing with minoTour.

2021 ◽  
Author(s):  
Rory James Munro ◽  
Nadine Holmes ◽  
Christopher Moore ◽  
Matthew Carlile ◽  
Alex Payne ◽  
...  
Keyword(s):  
Real Time ◽  
Phylogenetic Trees ◽  
Sequencing Data ◽  
Time Analysis ◽  
Real Time Analysis ◽  
Oxford Nanopore ◽  
Individual Snps ◽  
Wide Range ◽  
Time Required ◽  
Viral Sequencing

Motivation: The ongoing SARS-CoV-2 pandemic has demonstrated the utility of real-time analysis of sequencing data, with a wide range of databases and resources for analysis now available. Here we show how the real-time nature of Oxford Nanopore Technologies sequencers can accelerate consensus generation, lineage and variant status assignment. We exploit the fact that multiplexed viral sequencing libraries quickly generate sufficient data for the majority of samples, with diminishing returns on remaining samples as the sequencing run progresses. We demonstrate methods to determine when a sequencing run has passed this point in order to reduce the time required and cost of sequencing. Results: We extended MinoTour, our real-time analysis and monitoring platform for nanopore sequencers, to provide SARS-CoV2 analysis using ARTIC network pipelines. We additionally developed an algorithm to predict which samples will achieve sufficient coverage, automatically running the ARTIC medaka informatics pipeline once specific coverage thresholds have been reached on these samples. After testing on run data, we find significant run time savings are possible, enabling flow cells to be used more efficiently and enabling higher throughput data analysis. The resultant consensus genomes are assigned both PANGO lineage and variant status as defined by Public Health England. Samples from within individual runs are used to generate phylogenetic trees incorporating optional background samples as well as summaries of individual SNPs. As minoTour uses ARTIC pipelines, new primer schemes and pathogens can be added to allow minoTour to aid in real-time analysis of pathogens in the future.

scholarly journals Real-time analysis of nanopore-based metagenomic sequencing from orthopaedic device infection

2017 ◽  
Author(s):  
Nicholas D Sanderson ◽  
Teresa L Street ◽  
Dona Foster ◽  
Jeremy Swann ◽  
Bridget L. Atkins ◽  
...  
Keyword(s):  
Real Time ◽  
Sequence Data ◽  
Metagenomic Sequencing ◽  
Nanopore Sequencing ◽  
Time Analysis ◽  
Real Time Analysis ◽  
Joint Infections ◽  
Prosthetic Joint ◽  
Device Infection ◽  
Prosthetic Joint Infections

AbstractProsthetic joint infections are clinically difficult to diagnose and treat. Previously, we demonstrated metagenomic sequencing on an Illumina MiSeq replicates the findings of current gold standard microbiological diagnostic techniques. Nanopore sequencing offers advantages in speed of detection over MiSeq. Here, we compare direct-from-clinical-sample metagenomic Illumina sequencing with Nanopore sequencing, and report a real-time analytical pathway for Nanopore sequence data, designed for detecting bacterial composition of prosthetic joint infections.DNA was extracted from the sonication fluids of seven explanted orthopaedic devices, and additionally from two culture negative controls, and was sequenced on the Oxford Nanopore Technologies MinION platform. A specific analysis pipeline was assembled to overcome the challenges of identifying the true infecting pathogen, given high levels of host contamination and unavoidable background lab and kit contamination.The majority of DNA classified (>90%) was host contamination and discarded. Using negative control filtering thresholds, the species identified corresponded with both routine microbiological diagnosis and MiSeq results. By analysing sequences in real time, causes of infection were robustly detected within minutes from initiation of sequencing.We demonstrate initial proof of concept that metagenomic MinION sequencing can provide rapid, accurate diagnosis for prosthetic joint infections. We demonstrate a novel, scalable pipeline for real-time analysis of MinION sequence data. The high proportion of human DNA in extracts prevents full genome analysis from complete coverage, and methods to reduce this could increase genome depth and allow antimicrobial resistance profiling.

An Interactive Minicomputer Program for the Indexing and Simulation of Electron Diffraction Patterns

1976 ◽  
Vol 34 ◽  
pp. 542-543
Author(s):  
R.P. Goehner ◽  
W.T. Hatfield ◽  
Prakash Rao
Keyword(s):  
Electron Diffraction ◽  
Real Time ◽  
Pattern Analysis ◽  
Flow Diagram ◽  
Hard Copy ◽  
Time Analysis ◽  
Real Time Analysis ◽  
Transmission Electron ◽  
One Step ◽  
Diffraction Patterns

Computer programs are now available in various laboratories for the indexing and simulation of transmission electron diffraction patterns. Although these programs address themselves to the solution of various aspects of the indexing and simulation process, the ultimate goal is to perform real time diffraction pattern analysis directly off of the imaging screen of the transmission electron microscope. The program to be described in this paper represents one step prior to real time analysis. It involves the combination of two programs, described in an earlier paper(l), into a single program for use on an interactive basis with a minicomputer. In our case, the minicomputer is an INTERDATA 70 equipped with a Tektronix 4010-1 graphical display terminal and hard copy unit.A simplified flow diagram of the combined program, written in Fortran IV, is shown in Figure 1. It consists of two programs INDEX and TEDP which index and simulate electron diffraction patterns respectively. The user has the option of choosing either the indexing or simulating aspects of the combined program.

scholarly journals Real-Time Analysis of Animal Feeding Behavior With a Low-Calculation-Power CPU

2020 ◽  
Vol 67 (4) ◽  
pp. 1197-1205 ◽  
Author(s):  
Yuki Totani ◽  
Susumu Kotani ◽  
Kei Odai ◽  
Etsuro Ito ◽  
Manabu Sakakibara
Keyword(s):  
Feeding Behavior ◽  
Real Time ◽  
Time Analysis ◽  
Real Time Analysis ◽  
Animal Feeding

A threshold-based, real-time analysis in early detection of endpoint anomalies using SIEM expertise

2021 ◽  
Vol 2021 (4) ◽  
pp. 7-16
Author(s):  
Sivaraman Eswaran ◽  
Aruna Srinivasan ◽  
Prasad Honnavalli
Keyword(s):  
Early Detection ◽  
Real Time ◽  
Time Analysis ◽  
Real Time Analysis

Chromo-fluorogenic sensors for chemical warfare agents in real-time analysis: journey towards accurate detection and differentiation

2021 ◽  
Vol 57 (28) ◽  
pp. 3430-3444
Author(s):  
Vinod Kumar
Keyword(s):  
Real Time ◽  
Chemical Warfare Agents ◽  
Chemical Warfare ◽  
Chemical Probes ◽  
Time Analysis ◽  
Specific Detection ◽  
Success Stories ◽  
Real Time Analysis ◽  
Warfare Agents ◽  
Unique Chemical

This article describes our journey and success stories in the development of chemical warfare detection, detailing the range of unique chemical probes and methods explored to achieve the specific detection of individual agents in realistic environments.

scholarly journals A Framework for International Collaboration on ITER Using Large-Scale Data Transfer to Enable Near-Real-Time Analysis

2021 ◽  
Vol 77 (2) ◽  
pp. 98-108
Author(s):  
R. M. Churchill ◽  
C. S. Chang ◽  
J. Choi ◽  
J. Wong ◽  
S. Klasky ◽  
...  
Keyword(s):  
Real Time ◽  
International Collaboration ◽  
Large Scale ◽  
Data Transfer ◽  
Time Analysis ◽  
Real Time Analysis ◽  
Large Scale Data ◽  
Scale Data
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