Early sample tagging and pooling enables simultaneous SARS-CoV-2 detection and variant sequencing

  1. Alon Chappleboim
  2. Daphna Joseph-Strauss
  3. Ayelet Rahat
  4. Israa Sharkia
  5. Miriam Adam
  6. Daniel Kitsberg
  7. Gavriel Fialkoff
  8. Matan Lotem
  9. Omer Gershon
  10. Anna-Kristina Schmidtner
  11. Esther Oiknine-Djian
  12. Agnes Klochendler
  13. Ronen Sadeh
  14. Yuval Dor
  15. Dana Wolf
  16. Naomi Habib
  17. Nir Friedman

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Abstract

A sequencing-based detection and genotyping assay for SARS-CoV-2 is based on early sample pooling using barcoded oligo hybridization.

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  1. Version published to 10.1126/scitranslmed.abj2266
  2. Version published to 10.1101/2020.08.08.20170746v2 on medRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.08.08.20170746: (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
    NGS data analysis: Reads were demultiplexed using bcl2fastq (version 2.20.0) and further processed by ad-hoc python scripts that are available as jupyter notebooks.
    bcl2fastq
    suggested: (bcl2fastq , RRID:SCR_015058)
    python
    suggested: (IPython, RRID:SCR_001658)
    We used the python API of UMI-tools to cluster UMI sequences.
    UMI-tools
    suggested: (UMI-tools, RRID:SCR_017048)

    Results from OddPub: Thank you for sharing your code.

    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: 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.

    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.

  4. Version published to 10.1101/2020.08.08.20170746v1 on medRxiv