SARS-CoV-2 RECoVERY: a multi-platform open-source bioinformatic pipeline for the automatic construction and analysis of SARS-CoV-2 genomes from NGS sequencing data

De Sabato, L.; Vaccari, G.; Knijn, A.; Ianiro, G.; Di Bartolo, I.; Morabito, S.

doi:10.1101/2021.01.16.425365

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bioRxiv · 10.1101/2021.01.16.425365

SARS-CoV-2 RECoVERY: a multi-platform open-source bioinformatic pipeline for the automatic construction and analysis of SARS-CoV-2 genomes from NGS sequencing data

De Sabato, L.·Vaccari, G.·Knijn, A.·Ianiro, G.·Di Bartolo, I.·Morabito, S.

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Abstract

BackgroundSince its first appearance in December 2019, the novel Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2), spread worldwide causing an increasing number of cases and deaths (35,537,491 and 1,042,798, respectively at the time of writing, https://covid19.who.int). Similarly, the number of complete viral genome sequences produced by Next Generation Sequencing (NGS), increased exponentially. NGS enables a rapid accumulation of a large number of sequences. However, bioinformatics analyses are critical and require combined approaches for data analysis, which can be challenging for non-bioinformaticians. ResultsA user-friendly and sequencing platform-independent bioinformatics pipeline, named SARS-CoV-2 RECoVERY (REconstruction of CoronaVirus gEnomes & Rapid analYsis) has been developed to build SARS-CoV-2 complete genomes from raw sequencing reads and to investigate variants. The genomes built by SARS-CoV-2 RECoVERY were compared with those obtained using other software available and revealed comparable or better performances of SARS-CoV2 RECoVERY. Depending on the number of reads, the complete genome reconstruction and variants analysis can be achieved in less than one hour. The pipeline was implemented in the multi-usage open-source Galaxy platform allowing an easy access to the software and providing computational and storage resources to the community. ConclusionsSARS-CoV-2 RECoVERY is a piece of software destined to the scientific community working on SARS-CoV-2 phylogeny and molecular characterisation, providing a performant tool for the complete reconstruction and variants analysis of the viral genome. Additionally, the simple software interface and the ability to use it through a Galaxy instance without the need to implement computing and storage infrastructures, make SARS-CoV-2 RECoVERY a resource also for virologists with little or no bioinformatics skills. Availability and implementationThe pipeline SARS-CoV-2 RECoVERY (REconstruction of COronaVirus gEnomes & Rapid analYsis) is implemented in the Galaxy instance ARIES (https://aries.iss.it).

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De Sabato, L., Vaccari, G., Knijn, A., Ianiro, G., Di Bartolo, I., Morabito, S.. 2021-01-18. SARS-CoV-2 RECoVERY: a multi-platform open-source bioinformatic pipeline for the automatic construction and analysis of SARS-CoV-2 genomes from NGS sequencing data. https://doi.org/10.1101/2021.01.16.425365

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