Assessment of potential SARS-CoV-2 virus integration into human genome reveals no significant impact on RT-qPCR COVID-19 testing
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SciScore for 10.1101/2021.06.21.21258023: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Genome Assembly (PRL): For each specimen, sequencing adapters are first trimmed using Trim Galore v0.6.6 [31], then aligned to the SARS-CoV-2 Wuhan-Hu-1 reference genome (NCBI Nucleotide NC_045512.2) using BWA MEM 0.7.17-r1188 [32]. Trim Galoresuggested: (Trim Galore, RRID:SCR_011847)BWAsuggested: (BWA, RRID:SCR_010910)Consensus and mutations were called using samtools and Intrahost variant analysis of replicates (iVar) [33] with a minimum quality score of 20, frequency threshold of 0.6 and a minimum read … SciScore for 10.1101/2021.06.21.21258023: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Genome Assembly (PRL): For each specimen, sequencing adapters are first trimmed using Trim Galore v0.6.6 [31], then aligned to the SARS-CoV-2 Wuhan-Hu-1 reference genome (NCBI Nucleotide NC_045512.2) using BWA MEM 0.7.17-r1188 [32]. Trim Galoresuggested: (Trim Galore, RRID:SCR_011847)BWAsuggested: (BWA, RRID:SCR_010910)Consensus and mutations were called using samtools and Intrahost variant analysis of replicates (iVar) [33] with a minimum quality score of 20, frequency threshold of 0.6 and a minimum read depth of 10x coverage. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
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.
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