| Critical Commercial Assays |
|
| 2019-nCoV_N1 assay RT-qPCR assay |
(FDA https://www.fda.gov/media/134922/download) |
Cat # 2019-nCoVEUA-01 |
| NEB Luna Universal Probe One-Step Reaction Mix and Enzyme Mix |
(New England Biolabs, Herts, UK) |
Cat # E3006S |
| Applied Biosystems™ 7500 Fast PCR instrument running SDS software v2.3 |
(ThermoFisher Scientific) |
Cat # 4351106 |
|
| Deposited Data |
|
| GISAID |
(Shu and McCauley, 2017) |
https://www.gisaid.org |
| European Bioinformatics Institute |
(Rodriguez-Tomé and Stoehr, 1996) |
https://www.ebi.ac.uk/ |
| Issues with SARS CoV-2 Sequencing Data |
(De Maio et al.). |
https://github.com/W-L/ProblematicSites_SARS-CoV2/blob/master/problematic_sites_sarsCov2.vcf |
| A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology |
(Rambaut et al., 2020) |
https://cov-lineages.org/lineages/ |
|
| Oligonucleotides |
|
| ARTIC V3 primers |
https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv |
Available from IDT: https://eu.idtdna.com/pages/landing/coronavirus-research-reagents/ngs-assays
|
|
| Software and Algorithms |
|
| R 3.6.3 |
The R Foundation for Statistical Computing |
http://www.R-project.org |
| BEAST1 v1.10.5 |
(Suchard et al., 2018) |
https://beast.community/ |
| Tracer |
(Rambaut et al., 2018) |
https://beast.community/ |
| BEAST2 PhyDyn |
(Bouckaert et al., 2019; Volz and Siveroni, 2018) |
https://github.com/mrc-ide/PhyDyn |
| ARTIC network protocol |
ARTIC network |
https://artic.network/ncov-2019 |
| R packages (treedater 0.5.1, ape package v. 5.3, brms v. 2.13.5, rstan v. 2.21.2, SPIn v. 1.1, skygrowth 0.3.1) |
(Paradis and Schliep, 2019; Volz and Frost, 2017; Bürkner, 2018; Stan Development Team, 2020; Liu et al., 2015; Volz and Didelot, 2018) |
http://www.R-project.org; https://github.com/mrc-ide/skygrowth
|
| IQtree 1.6.12 |
(Minh et al., 2020; Rambaut et al., 2020) |
http://www.iqtree.org/ |
| MRC-CLIMB |
(Connor et al., 2016) |
https://www.climb.ac.uk/ |
| Nextflow pipeline for processing/assembly of ARTIC protocol amplicons |
https://github.com/connor-lab/ncov2019-artic-nf |
https://github.com/connor-lab/ncov2019-artic-nf |
