Table 1.
Sequencing and assembly statistics for the anaerobic digester sample using different technologies and approaches
| Illumina MiSeq | R9.4.1 / + Illumina | R10.4 / + Illumina | PacBio HiFi/ + Illumina | |
|---|---|---|---|---|
| Total yield (Gbp) | 13 | 35 | 14 | 15 |
| Read N50 (kbp) | 0.3 | 5.9 | 5.6 | 15.4 |
| Observed modal read accuracy (%)a | 100 | 96.77 | 98.11 | 99.93 |
| Assembly size (Mbp) | 409 | 754 | 379 | 606 |
| Contigs (>1 kbp) | 145,976 | 24,680 | 21,585 | 8,989 |
| Circular contigs (>0.5 Mbp) | 0 | 7 | 3 | 9 |
| Contig N50 (kbp) | 3.5 | 79.9 | 40.1 | 172.5 |
| Reads mapped to contigs (%) | 88.1 | 93.5 | 95.4 | 95.2 |
| HQ MAGs | 8 | 64/86 | 34/36 | 74/77 |
| MQ MAGs | 83 | 114/95 | 65/67 | 72/68 |
| No. of contigs per HQ MAG (median) | 184 | 15/16 | 21/21 | 9/10 |
| Single-contig HQ MAGs | 0 | 2/3 | 1/1 | 3/3 |
| Mapped reads in HQ MAGs (%) | 16 | 46/49 | 39/40 | 48/44 |
| Cost (US$)b | 1,200 | 811/2,011 | 811/2,011 | 4,420/5,620 |
| Cost per HQ MAG (US$) | 150 | 13/23 | 24/56 | 60/73 |
HQ, high quality.
xx/xx, short-read unpolished/polished assemblies, relevant only for MAG quality statistics because the overall assembly statistics are identical.
aObserved read accuracies calculated from read mappings to an Illumina-polished PacBio HiFi assembly.
bThe expenses encountered at the time of conducting the experiments. This may differ for other research groups.