Metagenome of a Bronchoalveolar Lavage Fluid Sample from a Confirmed COVID-19 Case in Quito, Ecuador, Obtained Using Oxford Nanopore MinION Technology
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Abstract
We report the metagenome analysis of a bronchoalveolar lavage (BAL) fluid sample from a confirmed COVID-19 case in Quito, Ecuador. Sequencing was performed using MinION technology.
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SciScore for 10.1101/2020.06.11.20128330: (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 HGSQ018 was collected from a 27 years old male patient who presented severe COVID-19 symptoms after a visit to Guayaquil and was admitted to the pneumology unit at HGSQ. Table 2: Resources
Software and Algorithms Sentences Resources Base calling of FAST5 files was performed using Guppy (version 3.4.5) (Wick, et al 2019), and the RAMPART software (v1.0.5) from the ARTIC Network (https://github.com/artic-network/rampart) was used to monitor sequencing in real-time. RAMPARTsuggested: (Rampart, RRID:SCR_016742)Metagenomic approach and bioinformatic … SciScore for 10.1101/2020.06.11.20128330: (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 HGSQ018 was collected from a 27 years old male patient who presented severe COVID-19 symptoms after a visit to Guayaquil and was admitted to the pneumology unit at HGSQ. Table 2: Resources
Software and Algorithms Sentences Resources Base calling of FAST5 files was performed using Guppy (version 3.4.5) (Wick, et al 2019), and the RAMPART software (v1.0.5) from the ARTIC Network (https://github.com/artic-network/rampart) was used to monitor sequencing in real-time. RAMPARTsuggested: (Rampart, RRID:SCR_016742)Metagenomic approach and bioinformatic analysis: cDNA MinION library preparation was performed using the Rapid Barcoding kit (SQK-RBK004) following manufacturer instructions. MinIONsuggested: (MinION, RRID:SCR_017985)The resulting library was loaded on an Oxford MinION flowcell (FLO-MIN 106) and sequenced using the MinKNOW version 4.05, for 24 hours. MinKNOWsuggested: NoneBasecalling and quality control analysis was performed using Guppy (version 3.4.5) and NanoPlot (version 1.29.0) respectively13. NanoPlotsuggested: NoneAdapters and barcodes were removed from the MinION reads using Porechop (version 0.2.4) (https://github.com/rrwick/Porechop). Porechopsuggested: (Porechop, RRID:SCR_016967)Finally, Samtools (version 1.9) (http://samtools.github.io) and Tablet alignment viewer (version 1.19.09.3) (https://ics.hutton.ac.uk/tablet) were used to visualize the mapped sequence. Samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)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.
- 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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