Tutorial: Investigating SARS-CoV-2 evolution and phylogeny using MNHN-Tree-Tools
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Abstract
The Covid-19 pandemic has caused at more than 3 million deaths by Mai this year [1]. It had a significant impact on the daily life and the global economy [2]. The virus has since its first recorded outbreak in China [3] mutated into new strains [4]. The Nextstrain [5] project has so far been monitoring the evolution of the virus. At the same time we were developing in our lab the MNHN-Tree-Tools [6] toolkit, primarily for the investigation of DNA repeat sequences. We have further extended MNHN-Tree-Tools [6] to guide phylogenetics. As such the toolkit has evolved into a high performance code, allowing for a fast investigation of millions of sequences. Given the context of the pandemic it became evident that we will use our versatile tool to investigate the evolution of SARS-CoV-2 sequences. Our efforts have cumulated in this tutorial that we share with the scientific community.
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SciScore for 10.1101/2021.12.21.473702: (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 Sentences Resources We instructed the NCBI website to prepare the data in FASTA format, containing only the SARS-CoV-2 Pango linage identifier as well as the NCBI accession code in the sequence identifier lines of the FASTA file. NCBIsuggested: (NCBI, RRID:SCR_006472)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.Resu…
SciScore for 10.1101/2021.12.21.473702: (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 Sentences Resources We instructed the NCBI website to prepare the data in FASTA format, containing only the SARS-CoV-2 Pango linage identifier as well as the NCBI accession code in the sequence identifier lines of the FASTA file. NCBIsuggested: (NCBI, RRID:SCR_006472)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.
- No funding statement was detected.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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