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  1. SciScore for 10.1101/2022.01.18.22269300: (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
    Rolling circle amplification and Sanger sequencing of the clones were performed by GeneWiz (New Jersey).
    GeneWiz
    suggested: (GENEWIZ, RRID:SCR_003177)
    Major and minor variant calling: We used the Galaxy SARS-CoV-2 variant calling pipeline for paired-end Illumina ARTIC amplicon data 21.
    Galaxy
    suggested: (Galaxy, RRID:SCR_006281)
    Briefly, the workflow performs quality control, masks primer sites, maps reads to reference using BMA-mem, calls variants using lofreq, annotates them using SNPEff, and outputs tabular variant call files, thresholded on minimum allele frequency of 0.05.
    SNPEff
    suggested: (SnpEff, RRID:SCR_005191)
    We tested 15 multiple sequence alignments, each containing all observed unique read fragment sequences spanning the S-gene (12 fragments) and N-gene (3 fragments) with three different four gamete tests: (1) the PHI test (implemented in RDP5 23,36) which considers sites with more than two alternative nucleotide states and uses a permutation-based test to determine whether detected site pairs displaying all four gametes display a degree of spatial clustering along the sequence that is significantly higher than would be expected in the absence of recombination; (2) the MCL recombination detection test (implemented in the pairwise component of the LDHat package; 24) which uses an approximate maximum likelihood method to infer the population scaled recombination rate needed to explain the observed numbers of site pairs with four gametes and then tests for significant deviation of the inferred recombination rate from zero using a permutation test, and (3) the RvsDist test (implemented in pairwise component of LDHat) which determines the correlation between the R2 measure of linkage disequilibrium between site pairs with four gametes with the physical distance in nucleotides between the site pairs 24 and uses a permutation test to detect significant deviations from the expected degree of correlation in the absence of recombination.
    LDHat
    suggested: (LDHAT, RRID:SCR_006298)
    These genomes were aligned to the Wuhan-Hu-1 reference genome (Genbank accession NC_045512.2) using MAFFT v7.453 (options --auto --keeplength -- addfragments) 33.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)

    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: 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.

    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.

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