Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases
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SciScore for 10.1101/2020.10.19.345702: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Sequence retrieval: In addition to our five COVID-19 metagenome sequences, we retrieved six (n=6) Chinese COVID-19 metagenome sequences from the NCBI (National Center for Biotechnology Information) database (https://www.ncbi.nlm.nih.gov/) (Accession numbers: SRX7705831-SRX7705836), four (n=4) shotgun metagenome sequences of human URTI belonged to CDC, USA from the NCBI (Accession numbers: SRR10252885, SRR10252888, SRR10252889 and SRR10252892 under bio-project: PRJNA573045), and … SciScore for 10.1101/2020.10.19.345702: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Sequence retrieval: In addition to our five COVID-19 metagenome sequences, we retrieved six (n=6) Chinese COVID-19 metagenome sequences from the NCBI (National Center for Biotechnology Information) database (https://www.ncbi.nlm.nih.gov/) (Accession numbers: SRX7705831-SRX7705836), four (n=4) shotgun metagenome sequences of human URTI belonged to CDC, USA from the NCBI (Accession numbers: SRR10252885, SRR10252888, SRR10252889 and SRR10252892 under bio-project: PRJNA573045), and six (n=6) metagenome sequences of human COPD from the European Nucleotide Archive, UK (Accession numbers: ERR2732537, ERR2732541, ERR2732559, ERR2732558, ERR2732551 and ERR2732550 under bio-project: PRJEB14074). https://www.ncbi.nlm.nih.gov/suggested: (GENSAT at NCBI - Gene Expression Nervous System Atlas, RRID:SCR_003923)Taxonomic abundance was determined by applying the ‘‘Best Hit Classification” option using the NCBI database as a reference with the following settings: maximum e-value of 1×10-30; minimum identity of 80% for bacteria, 60% for archaea and viruses, and a minimum alignment length of 20 as the set parameters. NCBIsuggested: (NCBI, RRID:SCR_006472)A ‘target’ genome library was constructed containing all viral sequences from the NCBI RefSeq Release 201 database ( RefSeqsuggested: (RefSeq, RRID:SCR_003496)https://en.wikipedia.org/wiki/National_Center_for_Biotechnology_Information) using the Kraken 2 (Wood et al., 2019), and the metagenomics reads were then aligned against the target library using the BWA algorithm (Jaillard et al., 2016). BWAsuggested: (BWA, RRID:SCR_010910)(KEGG) database (Kanehisa et al., 2019), and SEED subsystem identifiers (Glass et al., 2010) on the MG-RAST server using the partially modified set parameters (e-value cutoff: 1×10-30, min. % identity cutoff: 60%, and min. alignment length cutoff: 20). KEGGsuggested: (KEGG, RRID:SCR_012773)Comparative taxonomic and functional profiling was performed with the reference prokaryotic metagenomes available in MG-RAST database for statistical analyses. MG-RASTsuggested: (MG-RAST, RRID:SCR_004814)To identify differentially abundant SEED or KEGG functions, and resistance to antibiotics and toxic compounds (RATCs) across the four sampling locations (BD, China, UK and USA), statistical tests were applied with non-parametric test Kruskal-Wallis rank sum test at different KEGG and SEED subsystems levels IBM SPSS (SPSS, Version 23.0, IBM Corp., SPSSsuggested: (SPSS, RRID:SCR_002865)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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on page 53. 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.
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