VirusLab: A Tool for Customized SARS-CoV-2 Data Analysis
Since the beginning of 2020, the COVID-19 pandemic has posed unprecedented challenges to viral data analysis and connected host disease diagnostic methods. We propose VirusLab, a flexible system for analysing SARS-CoV-2 viral sequences and relating them to metadata or clinical information about the...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-11-01
|
| Series: | BioTech |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2673-6284/10/4/27 |
| _version_ | 1797410800468492288 |
|---|---|
| author | Pietro Pinoli Anna Bernasconi Anna Sandionigi Stefano Ceri |
| author_facet | Pietro Pinoli Anna Bernasconi Anna Sandionigi Stefano Ceri |
| author_sort | Pietro Pinoli |
| collection | DOAJ |
| description | Since the beginning of 2020, the COVID-19 pandemic has posed unprecedented challenges to viral data analysis and connected host disease diagnostic methods. We propose VirusLab, a flexible system for analysing SARS-CoV-2 viral sequences and relating them to metadata or clinical information about the host. VirusLab capitalizes on two existing resources: ViruSurf, a database of public SARS-CoV-2 sequences supporting metadata-driven search, and VirusViz, a tool for visual analysis of search results. VirusLab is designed for taking advantage of these resources within a server-side architecture that: (i) covers pipelines based on approaches already in use (ARTIC, Galaxy) but entirely cutomizable upon user request; (ii) predigests analysis of raw sequencing data from different platforms (Oxford Nanopore and Illumina); (iii) gives access to public archives datasets; (iv) supplies user-friendly reporting – making it a tool that can also be integrated into a business environment. VirusLab can be installed and hosted within the premises of any organization where information about SARS-CoV-2 sequences can be safely integrated with information about hosts (e.g., clinical metadata). A system such as VirusLab is not currently available in the landscape of similar providers: our results show that VirusLab is a powerful tool to generate tabular/graphical and machine readable reports that can be integrated in more complex pipelines. We foresee that the proposed system can support many research-oriented and therapeutic scenarios within hospitals or the tracing of viral sequences and their mutational processes within organizations for viral surveillance. |
| first_indexed | 2024-03-09T04:35:28Z |
| format | Article |
| id | doaj.art-01b40891ac15477e846bbd8f2303a078 |
| institution | Directory Open Access Journal |
| issn | 2673-6284 |
| language | English |
| last_indexed | 2024-03-09T04:35:28Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | BioTech |
| spelling | doaj.art-01b40891ac15477e846bbd8f2303a0782023-12-03T13:28:36ZengMDPI AGBioTech2673-62842021-11-011042710.3390/biotech10040027VirusLab: A Tool for Customized SARS-CoV-2 Data AnalysisPietro Pinoli0Anna Bernasconi1Anna Sandionigi2Stefano Ceri3Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milano, ItalyDipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milano, ItalyQuantia Consulting S.r.l., Mariano Comense, 22066 Como, ItalyDipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milano, ItalySince the beginning of 2020, the COVID-19 pandemic has posed unprecedented challenges to viral data analysis and connected host disease diagnostic methods. We propose VirusLab, a flexible system for analysing SARS-CoV-2 viral sequences and relating them to metadata or clinical information about the host. VirusLab capitalizes on two existing resources: ViruSurf, a database of public SARS-CoV-2 sequences supporting metadata-driven search, and VirusViz, a tool for visual analysis of search results. VirusLab is designed for taking advantage of these resources within a server-side architecture that: (i) covers pipelines based on approaches already in use (ARTIC, Galaxy) but entirely cutomizable upon user request; (ii) predigests analysis of raw sequencing data from different platforms (Oxford Nanopore and Illumina); (iii) gives access to public archives datasets; (iv) supplies user-friendly reporting – making it a tool that can also be integrated into a business environment. VirusLab can be installed and hosted within the premises of any organization where information about SARS-CoV-2 sequences can be safely integrated with information about hosts (e.g., clinical metadata). A system such as VirusLab is not currently available in the landscape of similar providers: our results show that VirusLab is a powerful tool to generate tabular/graphical and machine readable reports that can be integrated in more complex pipelines. We foresee that the proposed system can support many research-oriented and therapeutic scenarios within hospitals or the tracing of viral sequences and their mutational processes within organizations for viral surveillance.https://www.mdpi.com/2673-6284/10/4/27SARS-CoV-2data integrationvirus sequencingmutation analysisdiagnosticsCOVID-19 |
| spellingShingle | Pietro Pinoli Anna Bernasconi Anna Sandionigi Stefano Ceri VirusLab: A Tool for Customized SARS-CoV-2 Data Analysis BioTech SARS-CoV-2 data integration virus sequencing mutation analysis diagnostics COVID-19 |
| title | VirusLab: A Tool for Customized SARS-CoV-2 Data Analysis |
| title_full | VirusLab: A Tool for Customized SARS-CoV-2 Data Analysis |
| title_fullStr | VirusLab: A Tool for Customized SARS-CoV-2 Data Analysis |
| title_full_unstemmed | VirusLab: A Tool for Customized SARS-CoV-2 Data Analysis |
| title_short | VirusLab: A Tool for Customized SARS-CoV-2 Data Analysis |
| title_sort | viruslab a tool for customized sars cov 2 data analysis |
| topic | SARS-CoV-2 data integration virus sequencing mutation analysis diagnostics COVID-19 |
| url | https://www.mdpi.com/2673-6284/10/4/27 |
| work_keys_str_mv | AT pietropinoli viruslabatoolforcustomizedsarscov2dataanalysis AT annabernasconi viruslabatoolforcustomizedsarscov2dataanalysis AT annasandionigi viruslabatoolforcustomizedsarscov2dataanalysis AT stefanoceri viruslabatoolforcustomizedsarscov2dataanalysis |