Table 4. Comparison of Nanopore mapping data across library kits, United Kingdom, 2017a (n = 8 samples).
| Platform | Kit information |
Flow cell (FLO-) |
Virus identified |
Total reads (nt) |
% reads mapping |
% 20x coverage |
% 10x coverage |
Referenceb | Reference size (nt) |
Max de novo contig (nt) |
|---|---|---|---|---|---|---|---|---|---|---|
| Illumina | Nextera XT | NA | CHIKV | 1,391,258 | 95.23 | 98.86 | 99.37 | CHIKV | 11,826 | 7,321 |
| Illumina | Nextera XT | NA | DENV | 1,391,258 | 0.22 | 63.66 | 77.82 | DENV1 | 10,735 | 6,613 |
| MinION 2D | SQK-LSK208 | MIN106 | CHIKV | 1,891,028 | 85.12 | 99.73 | 99.91 | CHIKV | 11,826 | 10,793 |
| MinION 2D | SQK-LSK208 | MIN106 | DENV | 1,891,028 | 0.43 | 95.99 | 96.09 | DENV1 | 10,735 | 7,549 |
| MinION 1D2 | SQK-LSK308 | MIN107 | CHIKV | 5,080,906 | 74.50 | 99.94 | 100 | CHIKV | 11,826 | 11,369 |
| MinION 1D2 | SQK-LSK308 | MIN107 | DENV | 5,080,906 | 0.37 | 95.04 | 96.42 | DENV1 | 10,735 | 2,199 |
| MinION Rapid | SQK-RBK001 | MIN106 | CHIKV | 611,110 | 66.26 | 99.66 | 99.68 | CHIKV | 11,826 | 11,473 |
| MinION Rapid | SQK-RBK001 | MIN106 | DENV | 611,110 | 0.29 | 81.09 | 90.83 | DENV1 | 10,735 | 4,227 |
CHIKV: chikungunya virus; Ct: cycle threshold; DENV: dengue virus. NA: not applicable.
a Results presented in the table were obtained in 2017 on samples that had been collected and found positive for chikungunya or dengue virus by real-time reverse transcription-PCR in 2016.
b For DENV the serotype is also indicated.