Development and scaling of a sequencing pipeline for genomic surveillance of SARS-CoV-2 in New York City
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Abstract
In the ongoing COVID-19 pandemic, detecting the appearance and spread of variants of concern (VOC) is a critical capability in the fight to quell the virus and return to normalcy. Genomic surveillance of the emergence, propagation, and geographical spread of VOCs is thus an important tool for public health officials and government leaders to make policy decisions and advise the public. As part of our role as a major SARS-CoV-2 diagnostic testing facility in New York City, the Pandemic Response Lab (PRL) has been performing genomic surveillance on the large number of positive samples processed by the facility on a daily basis from throughout the New York metropolitan area. Here we describe the development and optimization of a high-throughput SARS-CoV-2 genome sequencing facility at PRL serving New York City.
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SciScore for 10.1101/2022.05.25.22273991: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources RNA Extraction of STAT samples at LIC R&D site: Reagent plates including binding plate, wash plate, 80% ethanol plate, and elution plate are prepared in advance for RNA extraction using ThermoScientific KingFisher Flex instrument. ThermoScientific KingFishersuggested: NoneSequencing STAT samples: A separate STAT pipeline was established at LIC in order to process high priority patient swabs sent directly from hospital emergency departments. STATsuggested: NoneGenome assembly and variant calling: For each … SciScore for 10.1101/2022.05.25.22273991: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources RNA Extraction of STAT samples at LIC R&D site: Reagent plates including binding plate, wash plate, 80% ethanol plate, and elution plate are prepared in advance for RNA extraction using ThermoScientific KingFisher Flex instrument. ThermoScientific KingFishersuggested: NoneSequencing STAT samples: A separate STAT pipeline was established at LIC in order to process high priority patient swabs sent directly from hospital emergency departments. STATsuggested: NoneGenome assembly and variant calling: For each specimen, sequencing adapters are first trimmed using Trim Galore v0.6.634, then aligned to the SARS-CoV-2 Wuhan-Hu-1 reference genome (NCBI Nucleotide NC_045512.2) using BWA MEM 0.7.17-r118835. Trim Galoresuggested: (Trim Galore, RRID:SCR_011847)BWAsuggested: (BWA, RRID:SCR_010910)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.
Results from scite Reference Check: We found no unreliable references.
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