On the many advantages of using the VariantExperiment class to store, exchange and analyze SARS-CoV-2 genomic data and associated metadata
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Abstract
On Friday, 19 March 2021, WHO organized a virtual global workshop highlighting the need for a globally coordinated plan to increase SARS-CoV-2 genetic sequencing capacities to detect SARS-CoV-2 mutations and variants, and to monitor virus genomic evolution worldwide. One week later, in another virtual meeting, it focused on sero epidemiology for SARS-CoV-2 variants of concern and variants of interest. Efficient monitoring of the virus relies on the storage, handling and sharing of the genomic data and the associated metadata. In this manuscript, we demonstrate how the Bioconductor VariantExperiment class addresses these needs, offering a robust and efficient solution to the requirements laid out by the WHO.
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SciScore for 10.1101/2021.04.05.438328: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources To this end, 10 fastq raw data files generated by the MinION Oxford Nanopore Technology (ONT) were downloaded from the European Nucleotide Archive (ENA) repository. MinIONsuggested: (MinION, RRID:SCR_017985)Data were mapped to the reference genome MN908947.3 with minimap2 2.17 [5] and SAM files were processed using samtools 1.9. [6] The calling of the mutations was performed using freebayes 1.3.2 [7]. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)After quality filtering with … SciScore for 10.1101/2021.04.05.438328: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources To this end, 10 fastq raw data files generated by the MinION Oxford Nanopore Technology (ONT) were downloaded from the European Nucleotide Archive (ENA) repository. MinIONsuggested: (MinION, RRID:SCR_017985)Data were mapped to the reference genome MN908947.3 with minimap2 2.17 [5] and SAM files were processed using samtools 1.9. [6] The calling of the mutations was performed using freebayes 1.3.2 [7]. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)After quality filtering with vcffilter, the resulting VCF file and a dummy metadata (including dummy patients characteristics as well as preanalytical, analytical and bioinformatics parameters) file were processed with the VariantExperiment and the VariantAnnotation packages in order to create the desired object of the VariantExperiment class. VariantAnnotationsuggested: NoneResults from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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