Exploring the coronavirus epidemic using the new WashU Virus Genome Browser
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Abstract
Since its debut in mid-December, 2019, the novel coronavirus (2019-nCoV) has rapidly spread from its origin in Wuhan, China, to several countries across the globe, leading to a global health crisis. As of February 7, 2020, 44 strains of the virus have been sequenced and uploaded to NCBI’s GenBank [1], providing insight into the virus’s evolutionary history and pathogenesis. Here, we present the WashU Virus Genome Browser, a web-based portal for viewing virus genomic data. The browser is home to 16 complete 2019-nCoV genome sequences, together with hundreds of related viral sequences including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and Ebola virus. In addition, the browser features unique customizability, supporting user-provided upload of novel viral sequences in various formats. Sequences can be viewed in both a track-based representation as well as a phylogenetic tree-based view, allowing the user to easily compare sequence features across multiple strains. The WashU Virus Genome Browser inherited many features and track types from the WashU Epigenome Browser, and additionally incorporated a new type of SNV track to address the specific needs of viral research. Our Virus Browser portal can be accessed at https://virusgateway.wustl.edu , and documentation is available at https://virusgateway.readthedocs.io/ .
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SciScore for 10.1101/2020.02.07.939124: (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 Sentences Resources Reference sequences, additional strains, and gene annotations: Genomic sequences of all viral strains were downloaded as FASTA files from NCBI [Supplementary Table 1]. NCBIsuggested: (NCBI, RRID:SCR_006472)To generate the phylogenetic trees, we used the MAFFT program, employing the fast option to align individual strains of each viral genome to its reference [10, 11]. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Phylogenetic trees were built using FastTree with the GTR model [12, 13]. FastTreesuggested: (FastTree, RRID:SCR_015501)Results from OddPub: Thank you for sharing your data.
Results from Li…SciScore for 10.1101/2020.02.07.939124: (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 Sentences Resources Reference sequences, additional strains, and gene annotations: Genomic sequences of all viral strains were downloaded as FASTA files from NCBI [Supplementary Table 1]. NCBIsuggested: (NCBI, RRID:SCR_006472)To generate the phylogenetic trees, we used the MAFFT program, employing the fast option to align individual strains of each viral genome to its reference [10, 11]. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Phylogenetic trees were built using FastTree with the GTR model [12, 13]. FastTreesuggested: (FastTree, RRID:SCR_015501)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 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:- No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
- 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.
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