Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins

SciScore for 10.1101/2020.02.13.945485: (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

Experimental Models: Cell Lines
Sentences	Resources
Using the intestine-lung mixed sample we were able to isolate a novel Betacoronavirus using the Vero-E6 cell line (Extended Data Figure S1).	Vero-E6 suggested: None
Software and Algorithms
Sentences	Resources
Both BLASTn and BLASTx were used to search against a local virus database, utilizing the data available at NCBI/GenBank.	BLASTn suggested: (BLASTN, RRID:SCR_001598) BLASTx suggested: (BLASTX, RRID:SCR_001653)
These reads were quality assessed, cleaned and assembled into contigs by both de novo (MEGAHIT v1.1.312) and using reference (BWA v0.7.1313) assembly methods, with …

SciScore for 10.1101/2020.02.13.945485: (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

Experimental Models: Cell Lines
Sentences	Resources
Using the intestine-lung mixed sample we were able to isolate a novel Betacoronavirus using the Vero-E6 cell line (Extended Data Figure S1).	Vero-E6 suggested: None
Software and Algorithms
Sentences	Resources
Both BLASTn and BLASTx were used to search against a local virus database, utilizing the data available at NCBI/GenBank.	BLASTn suggested: (BLASTN, RRID:SCR_001598) BLASTx suggested: (BLASTX, RRID:SCR_001653)
These reads were quality assessed, cleaned and assembled into contigs by both de novo (MEGAHIT v1.1.312) and using reference (BWA v0.7.1313) assembly methods, with BetaCoV/Wuhan/WIV04/2019 as reference.	MEGAHIT suggested: (MEGAHIT, RRID:SCR_018551) BWA suggested: (BWA, RRID:SCR_010910)
Liu et al. recently published a meta-transcriptomic study of pangolins7 and deposited 21 RNA-seq raw files on the SRA database (https://www.ncbi.nlm.nih.gov/sra).	https://www.ncbi.nlm.nih.gov/sra suggested: (NCBI Sequence Read Archive (SRA, RRID:SCR_004891)
We screened these raw read files using BLAST methods and found that five (SRR10168374, SRR10168376, SRR10168377, SRR10168378 and SRR10168392) contained reads that mapped to 2019-nCoV.	BLAST suggested: (BLASTX, RRID:SCR_001653)
These reads were subjected to quality assessment, cleaning and then de novo assembly using MEGAHIT12 and reference assembly using BWA13.	BWA13 suggested: None
We constructed a multiple sequence alignment of their complete genomes and individual genes using MAFFT v7.27314.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
Maximum likelihood phylogenies were estimated using PhyML v3.115, utilizing the GTR+I+Γ model of nucleotide substitution with 1,000 bootstrap replicates.	PhyML suggested: (PhyML, RRID:SCR_014629)

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:

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No protocol registration statement was detected.

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Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins

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