Catching SARS-CoV-2 by Sequence Hybridization: a Comparative Analysis
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Abstract
Sequencing the genomes of the circulating SARS-CoV-2 strains is the only way to monitor the viral spread and evolution of the virus. Two different approaches, namely, tiling multiplex PCR and sequence hybridization by bait capture, are commonly used to fulfill this task.
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SciScore for 10.1101/2021.02.05.429917: (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. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Cultivation and Purification of SARS-CoV-2: SARS-CoV-2 virus was cultured in Vero E6 cells with MEM containing 2% FBS at 37° C with 5% CO2 and was harvested 72 hours post infection. Vero E6suggested: NoneSoftware and Algorithms Sentences Resources For enrichment of the Twist libraries with either the SARS-CoV-2 specific or the Respiratory Panel, the manual “Twist Target Enrichment Protocol” was followed without any exception. SARS-CoV-2sugg…SciScore for 10.1101/2021.02.05.429917: (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. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Cultivation and Purification of SARS-CoV-2: SARS-CoV-2 virus was cultured in Vero E6 cells with MEM containing 2% FBS at 37° C with 5% CO2 and was harvested 72 hours post infection. Vero E6suggested: NoneSoftware and Algorithms Sentences Resources For enrichment of the Twist libraries with either the SARS-CoV-2 specific or the Respiratory Panel, the manual “Twist Target Enrichment Protocol” was followed without any exception. SARS-CoV-2suggested: (Active Motif Cat# 91351, RRID:AB_2847848)Data Analysis: Sequenced reads were cleaned from PCR duplicates using clumpify from the BBTools package40 prior subsampling them to 130,000 reads using seqtk41 to get normalized datasets for each pool. BBToolssuggested: (Bestus Bioinformaticus Tools, RRID:SCR_016968)The number of mapped reads were determined using samtools flagstat43 and coverage information was obtained using bedtools genomecov44. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)bedtoolssuggested: (BEDTools, RRID:SCR_006646)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
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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