SARS-CoV-2 infection dynamics revealed by wastewater sequencing analysis and deconvolution

Article activity feed

1. Version published to 10.1016/j.scitotenv.2022.158931

   Dec 1, 2022
2. 

   ScreenIT

   Dec 6, 2021

   SciScore for 10.1101/2021.11.30.21266952: (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
   The processed reads are aligned to the reference genome by BWA Mem [30] and various coverage statistics are taken by SAMtools coverage/bedcov [31].	BWA suggested: (BWA, RRID:SCR_010910) SAMtools suggested: (SAMTOOLS, RRID:SCR_002105)
   The alignment is used further for single nucleotide variant (SNV) calling using LoFreq [32].	LoFreq suggested: (LoFreq, RRID:SCR_013054)
   Figures and deconvolution plots are done with ggplot2 [39].	ggplot2 suggested: (ggplot2, RRID:SCR_014601)
   All details and code can be found on the pipelines repository: https://github.com/BIMSBbioinfo/pigx_sarscov2_ww Sample scoring …

   SciScore for 10.1101/2021.11.30.21266952: (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
   The processed reads are aligned to the reference genome by BWA Mem [30] and various coverage statistics are taken by SAMtools coverage/bedcov [31].	BWA suggested: (BWA, RRID:SCR_010910) SAMtools suggested: (SAMTOOLS, RRID:SCR_002105)
   The alignment is used further for single nucleotide variant (SNV) calling using LoFreq [32].	LoFreq suggested: (LoFreq, RRID:SCR_013054)
   Figures and deconvolution plots are done with ggplot2 [39].	ggplot2 suggested: (ggplot2, RRID:SCR_014601)
   All details and code can be found on the pipelines repository: https://github.com/BIMSBbioinfo/pigx_sarscov2_ww Sample scoring for quality check: With the provided BED file for the signature mutations listed in the mutation sheet a coverage analysis is performed using BEDtools coverage [40] within the pipeline.	BEDtools suggested: (BEDTools, RRID:SCR_006646)
   Reproducible environment: The presented results were produced using PiGx SARS-CoV-2 version 0.03 commit 2603b275106a2a96a422dcfba61554f4d9c0d780.	PiGx suggested: (PiGx, RRID:SCR_016476)

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

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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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   Results from scite Reference Check: We found no unreliable references.

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   Read the original source
3. 

   Version published to 10.1101/2021.11.30.21266952 on medRxiv

   Dec 2, 2021