1. SciScore for 10.1101/2022.01.10.22269041: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsIRB: 2.4 Ethical approval: The present study was approved by Institutional Ethics Committee (IEC) at Institute of Liver and Biliary Sciences, New Delhi (Ethical no. IEC/2020/77/MA07).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    Respiratory specimen from RT-PCR confirmed cases (November 25th to December 23rd 2021) which were being referred to our laboratory from designated districts of Delhi (South, South East, South West, East and West) as per the Government of National Capital Territory of Delhi (GNTCD) directives, were subjected to whole genome sequencing (WGS).
    suggested: None
    These raw files were converted, demultiplexed to fastq file using bcl2fastq (Illumina, v2.20) and were aligned against the SARS-CoV-2 reference genome (NC_045512.2).
    suggested: (bcl2fastq , RRID:SCR_015058)
    (https://www.gisaid.org). 2.2.2 Construction of phylogenetic tree: Using consensus FASTA generated from BaseSpace pipeline, the phylogenetic tree was build following the Nextstrain protcol for genetic epidemiology of SARS-CoV-2 using the reference genome of SARS-CoV-2 isolate named Wuhan-Hu-1 (NCBI Reference Sequence: NC_045512.2) (8).
    suggested: (BaseSpace, RRID:SCR_011881)
    2.5 Statistical analysis: Data recorded in the PIF was digitized for analysis using SPSS version 15 (IBM, Bangalore, South Asia).
    suggested: (SPSS, RRID:SCR_002865)

    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.

    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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