Variant analysis of SARS-CoV-2 genomes in the Middle East
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SciScore for 10.1101/2020.10.09.332692: (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 10 samples was selected as the optimum number to cover all possible countries and remain within alignment file limit of size 4 Mb (maximum size for Clustal Omega tool). Clustal Omega toolsuggested: NoneThe Clustal Omega online tool was used to perform the alignment (found at: https://www.ebi.ac.uk/Tools/msa/clustalo/). Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)SnpEff also predicts the effect of the variants. SnpEffsuggested: (SnpEff, RRID:SCR_005191)To create the SnpEff database, we downloaded data from NCBI for Wuhan reference NC_045512.2 and uploaded to Galaxy. Galaxysuggested:…SciScore for 10.1101/2020.10.09.332692: (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 10 samples was selected as the optimum number to cover all possible countries and remain within alignment file limit of size 4 Mb (maximum size for Clustal Omega tool). Clustal Omega toolsuggested: NoneThe Clustal Omega online tool was used to perform the alignment (found at: https://www.ebi.ac.uk/Tools/msa/clustalo/). Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)SnpEff also predicts the effect of the variants. SnpEffsuggested: (SnpEff, RRID:SCR_005191)To create the SnpEff database, we downloaded data from NCBI for Wuhan reference NC_045512.2 and uploaded to Galaxy. Galaxysuggested: (Galaxy, RRID:SCR_006281)The dplyr v0.8.4 package was used to summarise and align the data13. dplyrsuggested: (dplyr, RRID:SCR_016708)The ggplot2 package was used to align the identified variants and visualise the types of mutations that re-occur14. ggplot2suggested: (ggplot2, RRID:SCR_014601)We first select the file generated using BEAST and outputted the tree file. BEASTsuggested: (BEAST, RRID:SCR_010228)Then the output NEXUS file was imported to FigTree program to display. FigTreesuggested: (FigTree, RRID:SCR_008515)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 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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SciScore for 10.1101/2020.06.18.156810: (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 Sample filing: We performed multiple sequence alignments (MSA) using EMBOSS Clustal Omega8 and observed for conserved and consensus sequences to study the evolutionary relationship between the genomes. EMBOSSsuggested: (EMBOSS, RRID:SCR_008493)SNPeff, a genetic variant annotation program in the Galaxy server, was used to identify the protein level changes caused by SNPs11. SNPeffsuggested: (SnpEff, RRID:SCR_005191)Galaxysuggested: (Galaxy, RRID:SCR_006281)The genome database for … SciScore for 10.1101/2020.06.18.156810: (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 Sample filing: We performed multiple sequence alignments (MSA) using EMBOSS Clustal Omega8 and observed for conserved and consensus sequences to study the evolutionary relationship between the genomes. EMBOSSsuggested: (EMBOSS, RRID:SCR_008493)SNPeff, a genetic variant annotation program in the Galaxy server, was used to identify the protein level changes caused by SNPs11. SNPeffsuggested: (SnpEff, RRID:SCR_005191)Galaxysuggested: (Galaxy, RRID:SCR_006281)The genome database for both SARS-CoV-2 NC_045512.2 and SARS NC_004718 were built and compared using SNPeff, and Genbank7. SARS-CoV-2suggested: (Active Motif Cat# 91351, RRID:AB_2847848)(BEAST) v1.10.4, is used to perform Bayesian analysis of molecular sequences using MCMC14. BEASTsuggested: (BEAST, RRID:SCR_010228)The unrooted tree obtained from the models and the phylogenetic tree generated by Clustal Omega is used to predict the associations between samples. Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)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 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.
-