Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study

  1. Sanjeet Kumar
  2. Kanika Bansal

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  1. Version published to 10.1016/j.virusres.2021.198642
  2. ScreenIT

    SciScore for 10.1101/2021.08.11.455899: (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
    SentencesResources
    Multiple sequencing alignment (MSA) was performed using (MAFFT v7.467) (Nakamura, Yamada et al. 2018) (https://mafft.cbrc.jp/alignment/software/) which is based on fast fourier transform keeping NC 045512.2 (https://www.ncbi.nlm.nih.gov/genome/?term=NC_045512.2) (Wuhan-Hu-1) strain as reference.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    MSA obtained was used for the phylogenomic tree generation using fasttree v2.1.8 with double precision (Price, Dehal et al. 2010) with gamma time reversal method (gtr).
    fasttree
    suggested: (FastTree, RRID:SCR_015501)
    R library package seqinr (https://cran.r-project.org/web/packages/seqinr/index.html) and biostring package of bioconductor (https://bioconductor.org/packages/release/bioc/html/Biostrings.html) was used to get the list of mutational events in terms of nucleotide and protein.
    bioconductor
    suggested: (Bioconductor, RRID:SCR_006442)
    https://bioconductor.org/packages/release/bioc/html/Biostrings.html
    suggested: (Biostrings, RRID:SCR_016949)

    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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 16 and 17. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.08.11.455899v1 on bioRxiv