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Standardisation of COVID-19 data analysis to aid international research efforts

Standardisation of COVID-19 data analysis to aid international research efforts

08
Apr
Wed, 08/04/2020 - 09:19

Standardisation of COVID-19 data analysis to aid international research efforts

Pedro Duque, the Spanish Minister of Science & Innovation observing a nanopore sequencing device in a recent visit to CNAG-CRG.

Researchers at the Novoa Lab have launched a new database to advance the international research efforts studying COVID-19.  The publicly-available, free-to-use resource (https://covid.crg.eu) can be used by researchers from around the world to study how different variations of the virus grow, mutate and make proteins. 

To understand how the coronavirus grows, mutates and replicates, scientists have to sequence the RNA of COVID-19. The RNA sequence reveals crucial information about the proteins the virus makes to invade human cells and replicate, which in turn informs governments on the infectiousness and severity of the pandemic. 

Traditional sequencing tools can take a long time to provide results. In recent years, sequencing data in real time has become a reality thanks to the use of nanopore sequencing technologies, revolutionizing genomics research and disease outbreak monitoring. Nanopore sequencing provides scientists and clinicians with immediate access to the DNA and RNA sequence information of any living cell in real-time, enabling a rapid response against the threat of a pandemic. 

However, the raw data produced by nanopore sequencing is highly complex. Scientists and clinicians currently lack systematic guidelines for the reproducible analysis of the data, limiting the vast potential of the nascent technology.  

To standardize the analysis of publicly available SARS-CoV-2 nanopore sequencing data, the CRG is using MasterOfPores, a computer program developed by the group of Eva Novoa and CRG Bioinformatics Unit. 

MasterOfPores 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. The publicly-available, free-to-use resource has currently analysed 3TB of SARS-CoV-2 nanopore RNA sequencing data.

Related press release (27/03/2020): CRG standardises COVID-19 data analysis to aid international research efforts