Biology subjects

Munro, R. J.

Publications and source records attributed to Munro, R. J..

3 recordsLinked to original sources

bioRxiv2023

Icarust, a real-time simulator for Oxford Nanopore adaptive sampling.

1SummaryOxford Nanopore Technologies (ONT) sequencers enable real-time generation of sequence data, which allows for concurrent analysis during a run. Adaptive sampling leverages this real-time capability in extremis, rejecting or accepting reads for sequencing based on assessment of the sequence from the start of each read. This functionality is provided by ONTs software, MinKNOW (https://community.nanoporetech.com/downloads). Designing and developing software to take advantage of adaptive sampling can be expensive due to the cost of using real sequencing consumables, using precious samples and preparing sequencing libraries. MinKNOW addresses this issue in part by providing the ability to replay previously sequenced runs for testing, using its playback functionality. However, as we have illustrated here, the sequencing output only partially changes in response to adaptive sampling instructions. Here we present Icarust, a tool enabling more accurate approximations of sequencing runs. Icarust recreates all the required endpoints of MinKNOW to perform adaptive sampling and writes output compatible with current base-callers and analysis pipelines. Icarust is capable of serving nanopore signal to simulate a MinION or PromethION flow cell experiment from any reference genome using either R9 or R10 pore signal. We show that simulating sequencing runs with Icarust provides a realistic testing and development environment for software exploiting the real-time nature of Nanopore sequencing. Availability and ImplementationAll code is open source and freely available here - https://github.com/LooseLab/Icarust. Icarust is implemented in Rust, with an easy to install and use docker container available. Supplementary InformationSupplementary information is available here - https://github.com/Adoni5/Icarust_paper.

genomics↗

bioRxiv2021

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

MotivationThe 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. ResultsWe 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. Availability and ImplementationSource code and documentation is available at https://github.com/LooseLab/minotourapp. Supplementary informationSupplementary data are available from https://github.com/LooseLab/artic_minotour_analyses.

bioinformatics↗

bioRxiv2021

MinoTour, real-time monitoring and analysis for Nanopore Sequencers.

SummaryMinoTour offers a LIMS system for Oxford Nanopore Technology (ONT) sequencers, with real-time metrics and analysis available permanently for review. Integration of unique real-time automated analysis can reduce the time required to answer biological questions, including mapping and classification of sequence whilst a run is in progress. Real-time sequence data requires new methods of analysis which do not wait for the completion of a run and MinoTour provides a framework to allow users to exploit these features. Availability and ImplementationSource code and documentation are available at https://github.com/LooseLab/minotourcli and https://github.com/LooseLab/minotourapp. Docker images are available from https://hub.docker.com/r/adoni5/, and can be installed using a preconfigured docker-compose script at https://github.com/LooseLab/minotour-docker. An example server is available at http://137.44.59.170.

bioinformatics↗