Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations

  1. Karthik Gangavarapu
  2. Alaa Abdel Latif
  3. Julia L. Mullen
  4. Manar Alkuzweny
  5. Emory Hufbauer
  6. Ginger Tsueng
  7. Emily Haag
  8. Mark Zeller
  9. Christine M. Aceves
  10. Karina Zaiets
  11. Marco Cano
  12. Xinghua Zhou
  13. Zhongchao Qian
  14. Rachel Sattler
  15. Nathaniel L. Matteson
  16. Joshua I. Levy
  17. Raphael T. C. Lee
  18. Lucas Freitas
  19. Sebastian Maurer-Stroh
  20. GISAID Core and Curation Team
  21. Marc A. Suchard
  22. Chunlei Wu
  23. Andrew I. Su
  24. Kristian G. Andersen
  25. Laura D. Hughes

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  1. Version published to 10.1038/s41592-023-01769-3
  2. Version published to 10.21203/rs.3.rs-1723829/v1 on Research Square
  3. Version published to 10.1101/2022.01.27.22269965v2 on medRxiv
  4. ScreenIT

    SciScore for 10.1101/2022.01.27.22269965: (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
    A Tornado server is used to create API endpoints that leverage the search capabilities of Elasticsearch to perform complex aggregations of the underlying data.
    Tornado
    suggested: (ToRNADo, RRID:SCR_002706)

    Results from OddPub: Thank you for sharing your code and data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    We have tried to communicate these limitations through a dedicated “caveats” page with warnings regarding the interpretation of data interspersed throughout the interface. Lastly, to maximize the accessibility of the processed data, we also built an R package which can be used to authenticate against GISAID credentials and programmatically access the API, enabling researchers to access the data within R scripts for downstream analyses.

    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.

  5. Version published to 10.1101/2022.01.27.22269965v1 on medRxiv