Petabase-scale sequence alignment catalyses viral discovery
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SciScore for 10.1101/2020.08.07.241729: (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 Assigning a best-fit TaxID was not supported by any previously published taxonomy prediction software to the best of our knowledge; this requires assignment to intermediate ranks such as sub-genus and ranks below species (commonly called strains, but these ranks are not named in the Taxonomy database), and to unclassified taxa, e.g. TaxID 2724161, unclassified Buldecovirus, in cases where the genome is predicted to fall inside a named clade but outside all named taxa within that clade. Taxonomysuggested: (Taxonomy, RRID:SCR_004299)Records annoated as CoV were downloaded from UniProt [71], … SciScore for 10.1101/2020.08.07.241729: (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 Assigning a best-fit TaxID was not supported by any previously published taxonomy prediction software to the best of our knowledge; this requires assignment to intermediate ranks such as sub-genus and ranks below species (commonly called strains, but these ranks are not named in the Taxonomy database), and to unclassified taxa, e.g. TaxID 2724161, unclassified Buldecovirus, in cases where the genome is predicted to fall inside a named clade but outside all named taxa within that clade. Taxonomysuggested: (Taxonomy, RRID:SCR_004299)Records annoated as CoV were downloaded from UniProt [71], and chain sequences were extracted. UniProtsuggested: (UniProtKB, RRID:SCR_004426)For a given query genome, open reading frames (ORFs) are extracted using the EMBOSS getorf software [58]. EMBOSSsuggested: (EMBOSS, RRID:SCR_008493)For each domain, a multiple alignment of the top 16 matches plus query ORF is constructed on the fly by MUSCLE [72] and a neighbour-joining tree is inferred from the alignment, also using MUSCLE. MUSCLEsuggested: (MUSCLE, RRID:SCR_011812)We clustered the sequences to 99% identity using USEARCH ([46] USEARCHsuggested: (mubiomics, RRID:SCR_006785)To apply SerraPlace to a given genome, we first use HMMER ([59], v3.3) to generate a reference HMM, based on the reference alignment. HMMERsuggested: (Hmmer, RRID:SCR_005305)Results from OddPub: Thank you for sharing your code and data.
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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 29 and 6. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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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SciScore for 10.1101/2020.08.07.241729: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: Thank you for sharing your code and data.
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 Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: Please consider improving the rainbow (“jet”) colormap used on pages 6 and 29. At least one figure is not accessible to readers with …
SciScore for 10.1101/2020.08.07.241729: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: Thank you for sharing your code and data.
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 Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: Please consider improving the rainbow (“jet”) colormap used on pages 6 and 29. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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.
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