Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
No abstract available
Article activity feed
-
-
SciScore for 10.1101/2022.01.14.21267633: (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 Variants were then filtered with LoFreq and Bcftools 85 (v 1.9) only considering variants with a minimum coverage of 75 reads, a minimum Phred scaled calling quality value of 90 and InDels with a HRUN value of at less than 4. Phredsuggested: (Phred, RRID:SCR_001017)Variant annotation was performed with SnpEff 86 (v 4.3) and SnpSift 87 (v 4.3). SnpEffsuggested: (SnpEff, RRID:SCR_005191)If the SIMPLEX function does not converge, resort to the Beta function. SIMPLEXsuggested: (SIMPLEX, RRID:SCR_010807)Sequencing based tests were performed by partial sequencing of the spike gene 94, Sanger … SciScore for 10.1101/2022.01.14.21267633: (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 Variants were then filtered with LoFreq and Bcftools 85 (v 1.9) only considering variants with a minimum coverage of 75 reads, a minimum Phred scaled calling quality value of 90 and InDels with a HRUN value of at less than 4. Phredsuggested: (Phred, RRID:SCR_001017)Variant annotation was performed with SnpEff 86 (v 4.3) and SnpSift 87 (v 4.3). SnpEffsuggested: (SnpEff, RRID:SCR_005191)If the SIMPLEX function does not converge, resort to the Beta function. SIMPLEXsuggested: (SIMPLEX, RRID:SCR_010807)Sequencing based tests were performed by partial sequencing of the spike gene 94, Sanger sequencing or WGS. WGSsuggested: NoneThe method is implemented in a software tool named DeViVa (Deconvolution of Virus Variants), which was written in python (version 3.8) and which can be obtained from GitHub (https://github.com/SebH87/DeViVa). pythonsuggested: (IPython, RRID:SCR_001658)Nucleotide diversity: The loFreq filtered variant call format files of all WWTP for which more than 18 timepoints were available with at least 2/3 of the genome covered with more than ten reads, were used to extract variants with an allele frequency above 1%. loFreqsuggested: (LoFreq, RRID:SCR_013054)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.
- 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.
Results from scite Reference Check: We found no unreliable references.
-
