MINERVA: A Facile Strategy for SARS-CoV-2 Whole-Genome Deep Sequencing of Clinical Samples

  1. Chen Chen
  2. Jizhou Li
  3. Lin Di
  4. Qiuyu Jing
  5. Pengcheng Du
  6. Chuan Song
  7. Jiarui Li
  8. Qiong Li
  9. Yunlong Cao
  10. X. Sunney Xie
  11. Angela R. Wu
  12. Hui Zeng
  13. Yanyi Huang
  14. Jianbin Wang

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Abstract

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  1. Version published to 10.1016/j.molcel.2020.11.030
  2. ScreenIT

    SciScore for 10.1101/2020.04.25.060947: (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
    SentencesResources
    bioRxiv Online Publication ( 2020) . doi:10.1101/2020.03.16.993584 10 . Di , L . et al.
    bioRxiv
    suggested: (bioRxiv, SCR_003933)
    Clean data was aligned to GRCm38 genome and known transcript annotation using Tophat2 v2.1.1 .
    Tophat2
    suggested: None
    Ribosome-removed aligned reads were proceeded to calculate FPKM by Cufflinks v2.2.1 and gene body coverage by RSeQC v.2.6.4 .
    Cufflinks
    suggested: (Cufflinks, SCR_014597)
          <div style="margin-bottom:8px">
        <div><b>RSeQC</b></div>
        <div>suggested: (RSeQC, <a href="https://scicrunch.org/resources/Any/search?q=SCR_005275">SCR_005275</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data processing For metagenomic RNA-seq data , raw reads were quality controlled using BBmap ( version 38.68 ) and mapped to the human genome reference ( GRCh38 ) using STAR ( version 2.6.1d ) with default parameters .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>BBmap</b></div>
        <div>suggested: (BBmap, <a href="https://scicrunch.org/resources/Any/search?q=SCR_016965">SCR_016965</a>)</div>
      </div>
    
      <div style="margin-bottom:8px">
        <div><b>STAR</b></div>
        <div>suggested: (STAR, <a href="https://scicrunch.org/resources/Any/search?q=SCR_015899">SCR_015899</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All unmapped reads were collected using samtools ( version 1.3 ) for microbial taxonomy assignment by Centrifuge ( version 1.0.4) .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>samtools</b></div>
        <div>suggested: (SAMTOOLS, <a href="https://scicrunch.org/resources/Any/search?q=SCR_002105">SCR_002105</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Custom reference was built from all complete bacterial , viral and any assembled fungal genomes downloaded from NCBI RefSeq database ( viral and fungal genomes were downloaded on February 4th , 2020 , and bacterial genomes were downloaded on November 14th , 2018) .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>RefSeq</b></div>
        <div>suggested: (RefSeq, <a href="https://scicrunch.org/resources/Any/search?q=SCR_003496">SCR_003496</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For SARS-CoV-2 genome analysis, raw reads were trimmed to remove sequencing adaptors and low-quality bases with Cutadapt v1.15.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>Cutadapt</b></div>
        <div>suggested: (cutadapt, <a href="https://scicrunch.org/resources/Any/search?q=SCR_011841">SCR_011841</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Then we removed duplicates from the primary alignment with Picard Tools v2.17.6.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>Picard</b></div>
        <div>suggested: (Picard, <a href="https://scicrunch.org/resources/Any/search?q=SCR_006525">SCR_006525</a>)</div>
      </div>
    </td></tr></table>

    Results from OddPub: We did not find a statement about open data. We also did not find a statement about open code. Researchers are encouraged to share open data when possible (see Nature blog).

    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 is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2020.04.25.060947v2 on bioRxiv
  4. preLights

    Excerpt

    Learning from the past and preparing for the future: Development of a swift and easy RNA sequencing technique on rapidly evolving viral strains

  5. Version published to 10.1101/2020.04.25.060947v1 on bioRxiv