Table 4.
Comparison of the most important genome sequencing variables in Sanger (partial genome sequencing), and Illumina, MinION amplicon, and MinION direct (whole-genome sequencing).
| Sequence method | Partial sequencing | Whole-genome sequencing | ||
|---|---|---|---|---|
| Sanger (Chain termination method) | Massive parallel sequencing | MinION amplicon | MinION direct | |
| Platform | Applied Biosystems 3,500 XL Genetic Analyzer | Illumina (Illumina NovaSeq 6,000) | Nanopore (Mk1C) | Nanopore (Mk1C) |
| Costs of the instrument* | €143,600 | €850,000 | €4,410 | €4,410 |
| Costs per sample* | ≈€40 | ≈€300 | ≈€150 | ≈€100 |
| Time wetlab* | 27 h | 12 d† | 18 h | 14 h |
| Time drylab* | 1 h | 8 h | 6 h | 4 h |
| Space requirement | +++ | +++ | + | + |
| Virus-specific PCR required | Yes | No | Yes | No |
| Portable sequencer | No | No | Yes | Yes |
+ = low, ++ = medium, +++ = high.
*
Estimated time and costs are laboratory dependent.
†
As stated by Eurofins Genomics Europe Sequencing GmbH, 2022.