Target capture sequencing of SARS-CoV-2 genomes using the ONETest Coronaviruses Plus
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SciScore for 10.1101/2021.03.25.437083: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Ethics review: Approval for this study was obtained from the University of Florida Institutional Review Board (IRB202001328). Randomization Using seqtk v1.3 (https://github/com/lh3/seqtk), we randomly down-sampled (without replacement) the 2×150 nt reads of each ONETest library so that the resulting library had the same number of reads as the matched ARTIC library; each ONETest library was sub-sampled three times in this manner to generate three simulated replicates of the library. Blinding not detected. Power Analysis not detected. Sex as a biological variable Among the patients, 30 (43%) were male and 40 (57%) were female. Table 2: Resources
Software and Algorithms S… SciScore for 10.1101/2021.03.25.437083: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Ethics review: Approval for this study was obtained from the University of Florida Institutional Review Board (IRB202001328). Randomization Using seqtk v1.3 (https://github/com/lh3/seqtk), we randomly down-sampled (without replacement) the 2×150 nt reads of each ONETest library so that the resulting library had the same number of reads as the matched ARTIC library; each ONETest library was sub-sampled three times in this manner to generate three simulated replicates of the library. Blinding not detected. Power Analysis not detected. Sex as a biological variable Among the patients, 30 (43%) were male and 40 (57%) were female. Table 2: Resources
Software and Algorithms Sentences Resources Plus RealAmp Kit from OSANG Healthcare Co. Ltd., South Korea), which targets the RdRp, N, and E genes. OSANG Healthcaresuggested: NoneReads from these libraries were analyzed using a bioinformatics pipeline (v1.3.0; https://github.com/connor-lab/ncov2019-artic-nf) that automates the ARTIC data analysis protocol for Illumina reads (https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html), which utilizes bwa mem 15, samtools 16, and iVar 17. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Reads were discarded that mapped to the human genome sequence (GRCh38.p13, release 35) using bowtie2 v2.4.2 18. bowtie2suggested: (Bowtie 2, RRID:SCR_016368)The pipeline was implemented in C/C++ and Python using a combination of in-house software and third-party tools, including Biopython v1.78 19, bedtools v2.29.2 20, pybedtools v0.8.1 21, samtools/bcftools/htslib v1.11 16, and Snakemake v5.26.1 22. Pythonsuggested: (IPython, RRID:SCR_001658)Biopythonsuggested: (Biopython, RRID:SCR_007173)bedtoolssuggested: (BEDTools, RRID:SCR_006646)samtools/bcftools/htslibsuggested: NoneSnakemakesuggested: (Snakemake, RRID:SCR_003475)Visualization was done in R using ggplot2 23. ggplot2suggested: (ggplot2, RRID:SCR_014601)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.
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