|
Biological samples
|
|
|
| Residual NP swabs |
Emory Microbiology Lab |
N/A |
|
Critical commercial assays
|
| Nextera XT DNA Library Preparation kit |
illumina |
FC-131-1096 |
| illumina MiSeq kit |
illumina |
MS-102-3001 |
| Deposited data |
| SARS-CoV-2 consequence sequences |
This paper |
GISAID: PRJNA634356 |
| SARS-CoV-2 reads |
This paper |
NCBI: PRJNA634356 |
|
Software and algorithms
|
| Geneious |
|
https://www.geneious.com
|
| Nextstrain |
Hadfield et al., 2018
|
https://clades.nextstrain.org/
|
| IQtree |
Trifinopoulos et al., 2016 |
http://iqtree.cibiv.univie.ac.at/
|
| Interactive Tree of Life (iTOL) |
Letunic et al., 2021 |
https://itol.embl.de/
|
| ViReMA |
Routh et al., 2013 |
https://sourceforge.net/projects/virema/
|
| Pangolin |
Rambaut et al., 2020
|
https://pangolin.cog-uk.io
|
| Pilon |
Walker et al., 2014 |
https://github.com/broadinstitute/pilon
|
| Bowtie2 |
Langmead et al., 2012 |
http://bowtie-bio.sourceforge.net/index.shtml
|
| samtools |
Li et al., 2009 |
http://www.htslib.org/
|
| seqtk |
https://github.com/lh3/seatk
|
https://github.com/lh3/seqtk
|
| DESeq2 |
Love et al., 2014 |
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| R Studios |
RStudio: Integrated Development for R |
Rstudio.com
|
| SAS |
SAS Institute |
https://www.sas.com/enus/home.html
|
