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  1. SciScore for 10.1101/2022.05.12.22274799: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    Library sizes were evaluated using the Agilent BioAnalyzer 2100 and the high sensitivity dsDNA kit.
    Agilent BioAnalyzer
    suggested: None
    The Illumina sequencing adapters were removed, and low-quality bases were trimmed using AdapterRemoval (v2.3.1).
    suggested: (AdapterRemoval, RRID:SCR_011834)
    All remaining reads after host filtering were assigned taxonomy using Kraken2 (v2.1.1) with PlusPF database (release date: 1/27/2021).
    suggested: None
    For rRNA content estimation using Kraken2, a Kraken database (containing rRNA sequences from prokaryotes and eukaryotes) was built from the rRNA sequences collected from NCBI Nucleotide database using the following query: “biomol_rrna[PROP]” (as of March 17, 2021).
    suggested: (Kraken, RRID:SCR_005484)
    The 40M subsampled read pairs were mapped to the combined genome sequences using BWA-MEM (v0.7.17).
    suggested: (Sniffles, RRID:SCR_017619)
    For each species, the number of mapped reads and the number of total bases mapped were collected using Bedtools (v1.9) “multicov” and Samtools (v1.9) “depth” commands, respectively, with optional parameters “-d 0 -aa” being used for Samtools “depth” command to accurately report the depths in deeply covered regions.
    suggested: (BEDTools, RRID:SCR_006646)
    suggested: (SAMTOOLS, RRID:SCR_002105)
    AMR gene identification: The assembled contigs from the CZID workflow with 40M subsampled read pairs were retrieved and searched against AMR genes using NCBI AMRFinderPlus (v3.10.21)
    NCBI AMRFinderPlus
    suggested: None
    Within DEGenR, the raw read counts were imported, filtered, normalized using edgeR R-package to filter out any low-expressed genes.
    suggested: (edgeR, RRID:SCR_012802)
    The Enrichr R package (37) was used to rank enriched terms among DEGs using different databases and resources, including GO biological processes.
    suggested: (Enrichr, RRID:SCR_001575)

    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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