Estimating the relative proportions of SARS-CoV-2 haplotypes from wastewater samples

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1. Version published to 10.1016/j.crmeth.2022.100313

   Oct 1, 2022
2. 

   ScreenIT

   Jan 18, 2022

   SciScore for 10.1101/2022.01.13.22269236: (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
   Estimating the proportions of SARS-CoV-2 genomes: All sequencing reads are aligned to Wuhan-Hu-1 (NC_045512.2) using bowtie2 (Langmead and Salzberg, 2012) with the following command for single-end reads, bowtie2 –all -f -x wuhCor1 -U, and for paired-end reads, bowtie2 –all -f -x wuhCor1 −1 −2.	bowtie2 suggested: (Bowtie 2, RRID:SCR_016368)
   Applying the method to wastewater data from Crits-Christoph et al. (2021): Wastewater shotgun sequencing data from Crits-Christoph et al. (2021) was downloaded from NCBI BioProject ID PRJNA661613 …

   SciScore for 10.1101/2022.01.13.22269236: (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
   Estimating the proportions of SARS-CoV-2 genomes: All sequencing reads are aligned to Wuhan-Hu-1 (NC_045512.2) using bowtie2 (Langmead and Salzberg, 2012) with the following command for single-end reads, bowtie2 –all -f -x wuhCor1 -U, and for paired-end reads, bowtie2 –all -f -x wuhCor1 −1 −2.	bowtie2 suggested: (Bowtie 2, RRID:SCR_016368)
   Applying the method to wastewater data from Crits-Christoph et al. (2021): Wastewater shotgun sequencing data from Crits-Christoph et al. (2021) was downloaded from NCBI BioProject ID PRJNA661613 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA661613).	BioProject suggested: (NCBI BioProject, RRID:SCR_004801)
   All samples were pooled together and aligned against Wuhan-Hu-1 using BWA-MEM (Li, 2013) to identify SARS-CoV-2 reads.	BWA-MEM suggested: (Sniffles, RRID:SCR_017619)

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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 one unreliable citation. If you need to cite a retracted paper, we recommend noting at the beginning of the citation that the paper is retracted (i.e. RETRACTED: Title of paper, authors, journal, etc.).

   DOI	Status	Title
   10.1016/s0140-6736(20)31180-6	True	RETRACTED: Hydroxychloroquine or Chloroquine With or Without…

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3. 

   Version published to 10.1101/2022.01.13.22269236v2 on medRxiv

   Jan 14, 2022
4. 

   Version published to 10.1101/2022.01.13.22269236v1 on medRxiv

   Jan 13, 2022