Phylogenetic analysis of SARS-CoV-2 genomes in Turkey
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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 Sentences Resources We used Augur toolkit to align whole genome sequences using mafft algorithm (--reorder --anysymbol – nomemsave) (Katoh and Standley 2016). Augursuggested: NoneFor 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-TREEsuggested: (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. FigTreesuggested: (FigTree, RRID:SCR_008515)The GFF … 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 Sentences Resources We used Augur toolkit to align whole genome sequences using mafft algorithm (--reorder --anysymbol – nomemsave) (Katoh and Standley 2016). Augursuggested: NoneFor 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-TREEsuggested: (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. FigTreesuggested: (FigTree, RRID:SCR_008515)The GFF file of the reference genome (GCF_009858895.2) was extracted from NCBI Genome database. NCBI Genomesuggested: (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.
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