coronapp : A Web Application to Annotate and Monitor SARS-CoV-2 Mutations

  1. Daniele Mercatelli
  2. Luca Triboli
  3. Eleonora Fornasari
  4. Forest Ray
  5. Federico M. Giorgi

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Abstract

The avalanche of genomic data generated from the SARS-CoV-2 virus requires the development of tools to detect and monitor its mutations across the world. Here, we present a webtool, coronapp , dedicated to easily processing user-provided SARS-CoV-2 genomic sequences and visualizing current worldwide status of SARS-CoV-2 mutations.

The webtool allows users to highlight mutations and categorize them by frequency, country, genomic location and effect on protein sequences, and to monitor their presence in the population over time.

The tool is available at http://giorgilab.unibo.it/coronapp/ for the worldwide dataset and at http://giorgilab.unibo.it/coronannotator/ for the annotation of user-provided sequences. The full code is freely shared at https://github.com/federicogiorgi/giorgilab/tree/master/coronapp

Data Availability Statement

The data that support the findings of this study derive from the GISAID consortium and are openly available in Github, in Rdata format for the R environment, in files results.rda and metadata.rda, at the following link: https://github.com/federicogiorgi/giorgilab/tree/master/coronapp/data

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    SciScore for 10.1101/2020.05.31.124966: (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
    The results visualization utilizes both basic R functions and Shiny functionalities; for tooltip functionality, coronapp uses the R package googleVis v0.6.4, which provides an interface between R and the Google visualization API [19].
    googleVis
    suggested: None

    Results from OddPub: Thank you for sharing your code and 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 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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

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  2. Version published to 10.1101/2020.05.31.124966 on bioRxiv