Disentangling primer interactions improves SARS-CoV-2 genome sequencing by multiplex tiling PCR
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SciScore for 10.1101/2020.03.10.985150: (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 Design of alternative primers: Re-design of the primer nCoV-2019_76_RIGHT was done using PRIMER3 software (Untergasser et al. 2012). PRIMER3suggested: (Primer3, RRID:SCR_003139)Other primers were basically re-designed just by shifting their position several nucleotides toward the 5′ ends, but extension or trimming on either end were applied when the medium dissociation temperature (Tm) predicted by the NEB website tool (https://tmcalculator.neb.com/) were considered too low or … SciScore for 10.1101/2020.03.10.985150: (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 Design of alternative primers: Re-design of the primer nCoV-2019_76_RIGHT was done using PRIMER3 software (Untergasser et al. 2012). PRIMER3suggested: (Primer3, RRID:SCR_003139)Other primers were basically re-designed just by shifting their position several nucleotides toward the 5′ ends, but extension or trimming on either end were applied when the medium dissociation temperature (Tm) predicted by the NEB website tool (https://tmcalculator.neb.com/) were considered too low or high. https://tmcalculator.neb.com/suggested: (NEB Tm calculator, RRID:SCR_017969)The number of insert fragments overlapping each defined small representative region were counted by the co er ge function in the bedtools. bedtoolssuggested: (BEDTools, RRID:SCR_006646)Results 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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