Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand

Article activity feed

1. Version published to 10.3201/eid2705.204579

   May 1, 2021
2. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2020.10.28.20221853: (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
   Genomes assigned to the B.1.1.1. lineage (n = 4,544) were subsampled to include 1,996 most recent-in-time sequences along with four outgroup (non-B.1.1.1.) sequences, and were aligned with those from the recent New Zealand outbreak (n = 140) using MAFFT (v 7)22 employing the FFT-NS-2 progressive alignment algorithm.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   Bayesian phylogenetic analyses were performed using BEAST 2.523.	BEAST suggested: (BEAST, RRID:SCR_010228)
   Phylogenetic trees …

   SciScore for 10.1101/2020.10.28.20221853: (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
   Genomes assigned to the B.1.1.1. lineage (n = 4,544) were subsampled to include 1,996 most recent-in-time sequences along with four outgroup (non-B.1.1.1.) sequences, and were aligned with those from the recent New Zealand outbreak (n = 140) using MAFFT (v 7)22 employing the FFT-NS-2 progressive alignment algorithm.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   Bayesian phylogenetic analyses were performed using BEAST 2.523.	BEAST suggested: (BEAST, RRID:SCR_010228)
   Phylogenetic trees were annotated using FigTree (v 1.4)25 and Tree of Life (v 4)26.	FigTree suggested: (FigTree, RRID:SCR_008515)

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   Results from OddPub: Thank you for sharing your code.

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   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.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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.

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   Read the original source
3. 

   Version published to 10.1101/2020.10.28.20221853v1 on medRxiv

   Nov 3, 2020