Mutation signatures inform the natural host of SARS-CoV-2

  1. Shanjun Deng
  2. Ke Xing
  3. Xionglei He

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  1. Version published to 10.1093/nsr/nwab220
  2. ScreenIT

    SciScore for 10.1101/2021.07.05.451089: (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
    Phylogenetic analysis and mutation spectra calculation: The codon alignments of ORFs were performed based on amino acid sequences translated by TranslatorX29 and MAFFT v7.47130, and further concatenated by AMAS31 and refined with visual check.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Maximum likelihood phylogenetic analysis based on the whole coding regions was conducted by using IQ-TREE v2.0.332 with GTR+FO+R10 substitution model and 1,000 bootstrap replicates.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    Neighbor-Joining phylogeny was obtained in MEGA X33, which allows such analysis on synonymous sties, with 1,000 bootstrap replicates.
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)

    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.
    • 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 10.1101/2021.07.05.451089v1 on bioRxiv