Table 1.
Overview of the main sequencing platform characteristics used in this study.
| Illumina HiSeq 3000 | Ion Proton P1 | Ion S5 | DNBSEQ-G400 | DNBSEQ- T7 | ONT MinION R9 | PacBio Sequel II | |
|---|---|---|---|---|---|---|---|
| Amplification type | Solid-Phase bridge | emPCR | emPCR | DNB | DNB | — | — |
| Sequencing principle | SBS | SBS | SBS | SBS | SBS | SMS | SMS |
| Average reads length ± stdv after trimming (bp) | 149 ± 4.24 | 144.041 ± 28.43 | 145.76 ± 28.12 | 99.91 ± 0.96 | 99.52 ± 2.58 | 4408.41 ± 2831.95 | 10289.7 ± 4036.27 |
| Max read length after trimming (bp) | 150 | 373 | 347 | 100 | 100 | 60869 | 40278 |
| SE/PE | PE | SE | SE | PE | PE | SE | SE |
| Average insert size ± stdv (bp) | 433.47 ± 92.37 | — | — | 245.13 ± 51.04 | 235.56 ± 54.80 | — | — |
| Total Run Time | 4d | 4 h | 4 h | 3d | 3d | 48 h* | 30 h |
emPCR = emulsion PCR; SBS: Sequencing by Synthesis; SMS: Single-Molecule Sequencing; DNB: DNA NanoBall. *Data produced by MinION are accessible few minutes after the sequencing start, however, we run the MinION for 48 h to analyze the maximal throughput. DNBSEQ-G400 platform was formerly named MGISEQ-2000. SE: Single end (Forward read only). PE: Paired End. Run Time indicates time to obtain the maximal throughput.