TABLE 6.
Sequencing methods included on NCBI’s public SRA recordsa
| Method | # of sequences | # of labs | % of total |
|---|---|---|---|
| Enrichment kit | |||
| QIAseq DIRECT SARS-CoV-2 | 923 | 3 | 36.7 |
| NEBNext ARTIC SARS-CoV-2 RT-PCR Module | 825 | 12 | 32.8 |
| Illumina COVIDSeq Assay | 433 | 1 | 17.2 |
| Swift Normalase Amplicon SARS-COV-2 Panels | 199 | 1 | 7.9 |
| Not applicable | 137 | 4 | 5.4 |
| Amplicon PCR primer scheme | |||
| ARTIC V3 | 125 | 1 | 5.0 |
| ARTIC V4 | 308 | 1 | 12.2 |
| ARTIC V4.1 | 131 | 4 | 5.2 |
| NEB VarSkip 1 a Long | 18 | 1 | 0.7 |
| NEB VarSkip 1 a Short | 125 | 5 | 5.0 |
| NEB VarSkip 2 a Short | 307 | 8 | 12.2 |
| NEB VarSkip 2b Short | 369 | 7 | 14.7 |
| QIAseq DIRECT SARS-CoV-2—Boosted | 97 | 2 | 3.9 |
| QIAseq DIRECT SARS-CoV-2 primers | 838 | 3 | 33.3 |
| SARS-CoV-2 SNAP primer pool | 199 | 1 | 7.9 |
| Library preparation kit | |||
| Amplicon sequencing kit (PacBio) | 4 | 1 | 0.2 |
| Illumina DNA Prep | 513 | 8 | 20.4 |
| Ligation sequencing kit | 286 | 3 | 11.4 |
| NEBNext ARTIC SARS-CoV-2 Library Prep Kit (Illumina) | 514 | 5 | 20.4 |
| NEBNext Ultra II FS DNA Library Prep for Illumina | 6 | 1 | 0.2 |
| QIAseq DIRECT Unique Dual Index Prep | 995 | 4 | 39.5 |
| Swift Normalase Amplicon SARS-CoV-2 Panels | 199 | 1 | 7.5 |
| Sequencing instrument | |||
| Illumina iSeq 100 | 55 | 2 | 2.2 |
| Illumina MiniSeq | 440 | 4 | 17.5 |
| Illumina MiSeq | 1,622 | 14 | 64.4 |
| Illumina NovaSeq 6000 | 83 | 1 | 3.3 |
| NextSeq 550 | 57 | 1 | 2.3 |
| GridION | 8 | 1 | 0.3 |
| MinION | 248 | 1 | 9.9 |
| Sequel II | 4 | 1 | 0.2 |
a
Methods cover enrichment kit (general approach for enriching the target pathogen), Amplicon PCR primer scheme, library preparation kit, and sequencing instrument name.