SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies
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SciScore for 10.1101/2020.03.27.009480: (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
Software and Algorithms Sentences Resources We aligned the raw read data on reference strain MN975262.1 using bowtie2 [18], after quality check with FastQC (www.bioinformatics.bbsrc.ac.uk/projects/fastqc). bowtie2suggested: (Bowtie 2, RRID:SCR_016368)FastQCsuggested: (FastQC, RRID:SCR_014583)After removing PCR duplicates, SNVs were called with a Bonferroni-corrected P-value threshold of 0.05 using samtools [20] and LoFreq [21]. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)LoFreqsuggested: (LoFreq, RRID:SCR_013054)We … SciScore for 10.1101/2020.03.27.009480: (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
Software and Algorithms Sentences Resources We aligned the raw read data on reference strain MN975262.1 using bowtie2 [18], after quality check with FastQC (www.bioinformatics.bbsrc.ac.uk/projects/fastqc). bowtie2suggested: (Bowtie 2, RRID:SCR_016368)FastQCsuggested: (FastQC, RRID:SCR_014583)After removing PCR duplicates, SNVs were called with a Bonferroni-corrected P-value threshold of 0.05 using samtools [20] and LoFreq [21]. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)LoFreqsuggested: (LoFreq, RRID:SCR_013054)We annotated the variations to the reference strain using snpEff [22], SNVs effects were further filtered with snpSift [23] and we estimated the average mutation rate per gene across the viral genome using R scripts. snpEffsuggested: (SnpEff, RRID:SCR_005191)snpSiftsuggested: (SnpSift, RRID:SCR_015624)To investigate intra-host genomic rearrangements, we performed de novo assembly of the SARS-CoV-2 genomes using Spades [25], and the resulting contigs were analyzed with BLAST [26] and confirmed by remapping of the raw reads. Spadessuggested: (SPAdes, RRID:SCR_000131)BLASTsuggested: (BLASTX, RRID:SCR_001653)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:- No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
- No funding statement was detected.
- No protocol registration statement was detected.
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