Sequencing of SARS-CoV-2 genome using different nanopore chemistries

  1. Oscar González-Recio
  2. Mónica Gutiérrez-Rivas
  3. Ramón Peiró-Pastor
  4. Pilar Aguilera-Sepúlveda
  5. Cristina Cano-Gómez
  6. Miguel Ángel Jiménez-Clavero
  7. Jovita Fernández-Pinero

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Abstract

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  1. Version published to 10.1007/s00253-021-11250-w
  2. ScreenIT

    SciScore for 10.1101/2021.01.02.425072: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    DNA sequencing: The MinION device was used for ONT sequencing.
    MinION
    suggested: (MinION, RRID:SCR_017985)
    The flow cells were controlled and monitored using the MinKNOW software.
    MinKNOW
    suggested: None
    Data analysis: The FASTQ files were aligned against the NCBI-nr protein database (Nov. 2017) using DIAMOND v0.9.22 (blastx option) setting the -F option to 15, to consider frame-shift errors in the sequences and the -range Culling and -top options set to 10 to scan the whole sequence for alignments with a 10% of the best local bit score (megan.informatik.uni-tuebingen.de, accessed on October 2018).
    DIAMOND
    suggested: (DIAMOND, RRID:SCR_009457)
    The taxonomic binning of short reads from Illumina was performed using the daa2rma program from MEGAN Community Edition (CE) v6.11.
    MEGAN
    suggested: (MEGAN, RRID:SCR_011942)
    The total coverage of the genome for both sets of reads was calculated from the alignments using GenomeCoverageBed utility of the bedtools suite (Quinlan and Hall 2010), quantile-normalized and smoothed using a window width of 200bp.
    bedtools
    suggested: (BEDTools, RRID:SCR_006646)
    LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels from NGS data.
    LoFreq
    suggested: (LoFreq, RRID:SCR_013054)
    VarScan employs a robust heuristic/statistic approach to call variants that meet desired thresholds for read depth, base quality, variant allele frequency, and statistical significance.
    VarScan
    suggested: (VARSCAN, RRID:SCR_006849)
    Pilon identifies small variants with high accuracy as compared to state-of-the-art tools and is unique in its ability to accurately identify large sequence variants including duplications and resolve large insertions.
    Pilon
    suggested: (Pilon , RRID:SCR_014731)
    De-novo assembly: The de novo assembly was performed using Canu (Koren et al. 2017).
    Canu
    suggested: (Canu, RRID:SCR_015880)

    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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.01.02.425072v1 on bioRxiv