Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples
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SciScore for 10.1101/2020.12.01.405738: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Mapping to human transcriptome and genome were performed using STAR (ver 2.7) (41) and bwa mem (version 0.7.12-r1039) (42), respectively. STARsuggested: (STAR, RRID:SCR_015899)Read coverage was estimated using bedtools coverage from the bedtools suite (version v2.29.2) (43) for the portion of the viral genome targeted by the amplicons (positions 36-29,844 of the reference genome). bedtoolssuggested: (BEDTools, RRID:SCR_006646)Read subsampling was performed with samtools v1.9 (44). samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Statistical analysis: Statistical data analyses were performed … SciScore for 10.1101/2020.12.01.405738: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Mapping to human transcriptome and genome were performed using STAR (ver 2.7) (41) and bwa mem (version 0.7.12-r1039) (42), respectively. STARsuggested: (STAR, RRID:SCR_015899)Read coverage was estimated using bedtools coverage from the bedtools suite (version v2.29.2) (43) for the portion of the viral genome targeted by the amplicons (positions 36-29,844 of the reference genome). bedtoolssuggested: (BEDTools, RRID:SCR_006646)Read subsampling was performed with samtools v1.9 (44). samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Statistical analysis: Statistical data analyses were performed using the R software environment for statistical computing (46) and graphics with the ggplot2 package (47). ggplot2suggested: (ggplot2, RRID:SCR_014601)The datasets generated with synthetic SARS-CoV-2 genome and analysed during the current study are available in the Sequence Read Archive (SRA) repository under accession number SUB8654793. Sequence Read Archivesuggested: (DDBJ Sequence Read Archive, RRID:SCR_001370)Results from OddPub: Thank you for sharing your data.
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.
- No funding statement was detected.
- No protocol registration statement was detected.
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