Whole genome comparison of Pakistani Corona virus with Chinese and US Strains along with its predictive severity of COVID-19
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SciScore for 10.1101/2020.05.01.072942: (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 Pakistani FASTA sequences were converted to FastQ format using FASTA-to-Tabular-to-FASTQ tools (Galaxy Version Galaxysuggested: (Galaxy, RRID:SCR_006281)1.1.0) [11] and then mapped against reference genome using BWA MEM v 0.7.17.1 [12] BWAsuggested: (BWA, RRID:SCR_010910)Mapped reads were coordinate sorted using SortSam feature and duplicate sequences were marked using MarkDuplicate feature of Picard tool. Picardsuggested: (Picard, RRID:SCR_006525)SnpSift Variant type [14] and SnpEff eff was used to annotate variants by custom building of reference sequence databases using SnpEff build v … SciScore for 10.1101/2020.05.01.072942: (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 Pakistani FASTA sequences were converted to FastQ format using FASTA-to-Tabular-to-FASTQ tools (Galaxy Version Galaxysuggested: (Galaxy, RRID:SCR_006281)1.1.0) [11] and then mapped against reference genome using BWA MEM v 0.7.17.1 [12] BWAsuggested: (BWA, RRID:SCR_010910)Mapped reads were coordinate sorted using SortSam feature and duplicate sequences were marked using MarkDuplicate feature of Picard tool. Picardsuggested: (Picard, RRID:SCR_006525)SnpSift Variant type [14] and SnpEff eff was used to annotate variants by custom building of reference sequence databases using SnpEff build v 4.3+T.galaxy4 (Figure. 1) [15] SnpEffsuggested: (SnpEff, RRID:SCR_005191)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.
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