SARS-CoV-2 introduction and lineage dynamics across three epidemic peaks in Southern Brazil: massive spread of P.1
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SciScore for 10.1101/2021.07.29.454323: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: This study was approved by the Ethics Committee of Universidade Federal de Ciências da Saúde de Porto Alegre (Protocol n. 3.978.647, CAAE 30714520.0.0000.5345). 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 Bioinformatic analysis: Raw fastq files were trimmed to remove adapter sequences and low-quality reads using trimmomatic [13] (Parameters: leading:3 trailing:3 slidingwindow:4:25 minlen:36 illuminaclip: TruSeq3-PE.fa:2:30:10). trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)The quality of the resulting mapped BAM files was checked using Qualimap [15]. Qualim…SciScore for 10.1101/2021.07.29.454323: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: This study was approved by the Ethics Committee of Universidade Federal de Ciências da Saúde de Porto Alegre (Protocol n. 3.978.647, CAAE 30714520.0.0000.5345). 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 Bioinformatic analysis: Raw fastq files were trimmed to remove adapter sequences and low-quality reads using trimmomatic [13] (Parameters: leading:3 trailing:3 slidingwindow:4:25 minlen:36 illuminaclip: TruSeq3-PE.fa:2:30:10). trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)The quality of the resulting mapped BAM files was checked using Qualimap [15]. Qualimapsuggested: (QualiMap, RRID:SCR_001209)The software iVar (v1.2.2) was used to trim QIASEQ SARS-CoV-2 Primer Panel sequences and along with Samtools (v1.6) mpileup function [16] to variant calling (parameters: -A -d 20000 -Q 0) and consensus sequence generation (parameters: -q 20 -t 0). Samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Analyses were carried out using Nextstrain ncov workflow (https://github.com/) (default parameters), which includes alignment, phylogenetic reconstruction, geographic and ancestral trait reconstruction, and inference of transmission events. https://github.com/suggested: (Laubach Lab GitHub Repository project, RRID:SCR_021464)Nextstrain uses by default the software IQ-Tree and the substitution model GTR. IQ-Treesuggested: (IQ-TREE, RRID:SCR_017254)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.
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