De Novo-Whole Genome Assembly of the Roborovski Dwarf Hamster ( Phodopus roborovskii ) Genome: An Animal Model for Severe/Critical COVID-19
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Abstract
The Roborovski dwarf hamster Phodopus roborovskii belongs to the Phodopus genus, one of the seven within Cricetinae subfamily. Like other rodents such as mice, rats, or ferrets, hamsters can be important animal models for a range of diseases. Whereas the Syrian hamster from the genus Mesocricetus is now widely used as a model for mild-to-moderate coronavirus disease 2019, Roborovski dwarf hamster shows a severe-to-lethal course of disease upon infection with the novel human coronavirus severe acute respiratory syndrome coronavirus 2.
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SciScore for 10.1101/2021.10.02.462569: (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 De novo genome assembly: Raw unprocessed reads were assembled using Canu assembler (Koren et al. 2017) with an estimated genome size of 2.1gb and default parameters. Canusuggested: (Canu, RRID:SCR_015880)For evaluation of assembly quality and polishing effects, we applied the quality assessment tools QUAST (Mikheenko et al. 2018) and BUSCO (Simão et al. 2015) for estimation of genome completeness. BUSCOsuggested: (BUSCO, RRID:SCR_015008)Contigs classified as bacteria were removed and those classified as human were further analyzed using BLASTN (Altschul et al. 1990) with database nt to … SciScore for 10.1101/2021.10.02.462569: (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 De novo genome assembly: Raw unprocessed reads were assembled using Canu assembler (Koren et al. 2017) with an estimated genome size of 2.1gb and default parameters. Canusuggested: (Canu, RRID:SCR_015880)For evaluation of assembly quality and polishing effects, we applied the quality assessment tools QUAST (Mikheenko et al. 2018) and BUSCO (Simão et al. 2015) for estimation of genome completeness. BUSCOsuggested: (BUSCO, RRID:SCR_015008)Contigs classified as bacteria were removed and those classified as human were further analyzed using BLASTN (Altschul et al. 1990) with database nt to eliminate possible contamination with human genetic material. BLASTNsuggested: (BLASTN, RRID:SCR_001598)Genome annotation: RNA-Seq reads were quality trimmed and adapter sequences were removed with Cutadapt (Martin 2011) and filtered reads were mapped to the final polished assembly using the mapper STAR (Dobin et al. 2013). STARsuggested: (STAR, RRID:SCR_004463)The mapped reads, together with closely related reference genomes and annotations of Mus musculus (GRCm38.102), Rattus norvegicus (Rnor_6.0.102) and Mesocricetus auratus (MesAur1.0.100) - obtained from ENSEMBL - were used a input for the hybrid genome annotation tool GeMoMa (Keilwagen et al. 2016, 2018) to predict gene loci. GeMoMasuggested: (GeMoMa, RRID:SCR_017646)Finally, resulting gff files were converted to gtf format using GffRead (Pertea & Pertea 2020) and augmented with the original gene name(s) of the associated gene from the reference genomes with a custom Python script. Pythonsuggested: (IPython, RRID:SCR_001658)Results from OddPub: Thank you for sharing your 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: 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.
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Results from scite Reference Check: We found no unreliable references.
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