Phylogenetic analysis of SARS-CoV-2 genomes in Turkey

  1. Ogün ADEBALİ
  2. Aylin BİRCAN
  3. Defne ÇİRCİ
  4. Burak İŞLEK
  5. Zeynep KILINÇ
  6. Berkay SELÇUK
  7. Berk TURHAN

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Abstract

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  1. Version published to 10.3906/biy-2005-35
  2. Version published to 10.1101/2020.05.15.095794v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.05.15.095794: (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
    We used Augur toolkit to align whole genome sequences using mafft algorithm (--reorder --anysymbol – nomemsave) (Katoh and Standley 2016).
    Augur
    suggested: None
    For the sample EPI-ISL-428718 we additionally built a separate maximum likelihood phylogenetic tree by using IQ-TREE multicore version 1.6.1 with Ultra-fast Bootstrapping option and 1000 bootstraps.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    The tree was visualized in FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/), and rerooted by selecting EPI_ISL_428718 as an outgroup.
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    The GFF file of the reference genome (GCF_009858895.2) was extracted from NCBI Genome database.
    NCBI Genome
    suggested: (NCBI Genome, RRID:SCR_002474)

    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: We detected the following sentences addressing limitations in the study:
    We aim to eliminate the technical limitations (because of the size) by applying filtering methods without losing any relevant information.

    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.

  4. Version published to 10.1101/2020.05.15.095794v1 on bioRxiv