%0 Journal Article %T sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs %+ Physique pour la médecine (PhysMed Paris) %+ Physique Statistique et Inférence pour la Biologie %+ Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB %+ Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)) %+ Laboratoire d’innovation : vaccins – Innovation lab : vaccines %+ Laboratoire commun Pasteur-TheraVectys %+ Memorial Sloane Kettering Cancer Center [New York] %+ Weill Cornell Medicine [Cornell University] %A Di Gioacchino, Andrea %A Legendre, Rachel %A Rahou, Yannis %A Najburg, Valérie %A Charneau, Pierre %A Greenbaum, Benjamin %A Tangy, Frédéric %A van Der Werf, Sylvie %A Cocco, Simona %A Komarova, Anastassia %Z We acknowledge the ANR (Agence Nationale de la Recherche) and FRM (Fondation de la Recherche Médicale) for funding this work through the AAP Flash-Covid 19 project SARS-Cov-2immunRNAs. A.V.K. received support from ANR through the grant ANR-LBX-62 IBEID CoV-2SENSING/COVID 19. RNA NGS has been supported by France Génomique (ANR-10-INBS-09-09). %< avec comité de lecture %@ 1355-8382 %J RNA %I Cold Spring Harbor Laboratory Press %V 28 %N 3 %P 277-289 %8 2021-12-22 %D 2021 %R 10.1261/rna.078969.121 %M 34937774 %K subgenomic RNA %K SARS-CoV-2 %K defective viral genomes %K user-friendly bioinformatics %Z Computer Science [cs]/Bioinformatics [q-bio.QM] %Z Life Sciences [q-bio]/Santé publique et épidémiologie %Z Life Sciences [q-bio]/Microbiology and Parasitology/VirologyJournal articles %X Coronavirus RNA-dependent RNA polymerases produce subgenomic RNAs (sgRNAs) that encode viral structural and accessory proteins. User-friendly bioinformatic tools to detect and quantify sgRNA production are urgently needed to study the growing number of next-generation sequencing (NGS) data of SARS-CoV-2. We introduced sgDI-tector to identify and quantify sgRNA in SARS-CoV-2 NGS data. sgDI-tector allowed detection of sgRNA without initial knowledge of the transcription-regulatory sequences. We produced NGS data and successfully detected the nested set of sgRNAs with the ranking M > ORF3a > N>ORF6 > ORF7a > ORF8 > S > E>ORF7b. We also compared the level of sgRNA production with other types of viral RNA products such as defective interfering viral genomes. %G English %Z We would like to thank J. Pipoli da Fonseca, L. Lemée from Biomics Platform, C2RT, Institut Pasteur, Paris, France for RNA NGS, IBISA and the Illumina COVID-19 Projects’ offer. The authors would like to thank members of the Tangy, van der Werf laboratories and the National Reference Center (CNR) for Respiratory Viruses at the Institut Pasteur for support and valuable discussions. %2 https://pasteur.hal.science/pasteur-03591131/document %2 https://pasteur.hal.science/pasteur-03591131/file/RNA-2022-Di%20Gioacchino-277-89.pdf %L pasteur-03591131 %U https://pasteur.hal.science/pasteur-03591131 %~ INSERM %~ PASTEUR %~ ENS-PARIS %~ ESPCI %~ CNRS %~ SANTE_PUB_INSERM %~ PARISTECH %~ PSL %~ SORBONNE-UNIVERSITE %~ SORBONNE-UNIV %~ LPENS %~ UNIV-PARIS %~ UNIVERSITE-PARIS %~ UP-SCIENCES %~ ENS-PSL %~ ESPCI-PSL %~ SU-TI %~ ANR %~ ALLIANCE-SU %~ FRM %~ PASTEUR_UMR3569 %~ GMV-ARN %~ FRANCE-GENOMIQUE %~ BIOMICS_IP %~ BIOINFO_BIOSTAT_HUB