tetano
Editor, Senior Moderator
Life Sci Alliance
. 2023 Sep 25;6(12):e202302017.
doi: 10.26508/lsa.202302017. Print 2023 Dec. Comparative analysis of bioinformatics tools to characterize SARS-CoV-2 subgenomic RNAs
Denise Lavezzari[SUP] 1 [/SUP], Antonio Mori[SUP] 1 [/SUP], Elena Pomari[SUP] 2 [/SUP], Michela Deiana[SUP] 1 [/SUP], Antonio Fadda[SUP] 3 [/SUP], Luca Bertoli[SUP] 3 [/SUP], Alessandro Sinigaglia[SUP] 4 [/SUP], Silvia Riccetti[SUP] 4 [/SUP], Luisa Barzon[SUP] 4 [/SUP], Chiara Piubelli[SUP] 1 [/SUP], Massimo Delledonne[SUP] 3 [/SUP], Maria Rosaria Capobianchi[SUP] 1 [/SUP], Concetta Castilletti[SUP] 1 [/SUP]
Affiliations
During the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), positive-sense genomic RNA and subgenomic RNAs (sgRNAs) are synthesized by a discontinuous process of transcription characterized by a template switch, regulated by transcription-regulating sequences (TRS). Although poorly known about makeup and dynamics of sgRNAs population and function of its constituents, next-generation sequencing approaches with the help of bioinformatics tools have made a significant contribution to expand the knowledge of sgRNAs in SARS-CoV-2. For this scope to date, Periscope, LeTRS, sgDI-tector, and CORONATATOR have been developed. However, limited number of studies are available to compare the performance of such tools. To this purpose, we compared Periscope, LeTRS, and sgDI-tector in the identification of canonical (c-) and noncanonical (nc-) sgRNA species in the data obtained with the Illumina ARTIC sequencing protocol applied to SARS-CoV-2-infected Caco-2 cells, sampled at different time points. The three software showed a high concordance rate in the identification and in the quantification of c-sgRNA, whereas more differences were observed in nc-sgRNA. Overall, LeTRS and sgDI-tector result to be adequate alternatives to Periscope to analyze Fastq data from sequencing platforms other than Nanopore.
. 2023 Sep 25;6(12):e202302017.
doi: 10.26508/lsa.202302017. Print 2023 Dec. Comparative analysis of bioinformatics tools to characterize SARS-CoV-2 subgenomic RNAs
Denise Lavezzari[SUP] 1 [/SUP], Antonio Mori[SUP] 1 [/SUP], Elena Pomari[SUP] 2 [/SUP], Michela Deiana[SUP] 1 [/SUP], Antonio Fadda[SUP] 3 [/SUP], Luca Bertoli[SUP] 3 [/SUP], Alessandro Sinigaglia[SUP] 4 [/SUP], Silvia Riccetti[SUP] 4 [/SUP], Luisa Barzon[SUP] 4 [/SUP], Chiara Piubelli[SUP] 1 [/SUP], Massimo Delledonne[SUP] 3 [/SUP], Maria Rosaria Capobianchi[SUP] 1 [/SUP], Concetta Castilletti[SUP] 1 [/SUP]
Affiliations
- PMID: 37748810
- DOI: 10.26508/lsa.202302017
During the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), positive-sense genomic RNA and subgenomic RNAs (sgRNAs) are synthesized by a discontinuous process of transcription characterized by a template switch, regulated by transcription-regulating sequences (TRS). Although poorly known about makeup and dynamics of sgRNAs population and function of its constituents, next-generation sequencing approaches with the help of bioinformatics tools have made a significant contribution to expand the knowledge of sgRNAs in SARS-CoV-2. For this scope to date, Periscope, LeTRS, sgDI-tector, and CORONATATOR have been developed. However, limited number of studies are available to compare the performance of such tools. To this purpose, we compared Periscope, LeTRS, and sgDI-tector in the identification of canonical (c-) and noncanonical (nc-) sgRNA species in the data obtained with the Illumina ARTIC sequencing protocol applied to SARS-CoV-2-infected Caco-2 cells, sampled at different time points. The three software showed a high concordance rate in the identification and in the quantification of c-sgRNA, whereas more differences were observed in nc-sgRNA. Overall, LeTRS and sgDI-tector result to be adequate alternatives to Periscope to analyze Fastq data from sequencing platforms other than Nanopore.