Table 1.
Quality Control thresholds for isolate sequencing data.
| Quality Metric. | Salmonella enterica | Listeria monocytogenes | Escherichia coli | Campylobacter spp. |
|---|---|---|---|---|
| Q-score | ≥30 a | |||
| Average coverage depth | ≥30 a | ≥20 a | ≥40 a | ≥20 a |
| Assembly length [Mbp] | 4.5–5.1 e | 2.8–3.2 e | 4.5–5.6 e | 1.4–2.0 e |
| Number of contigs | 42–216 b | 18–212 b | 116–618 b | 15–112 b |
| Species purity [%] | >95 c,d | |||
| GC content [%] | 48.1–56.1 e | 33.9–41.9 e | 42.6–54.6 e | 26.4–35.3 e |
| Unique BUSCOs [%] | >95 c | >79 b | ||
| Duplicate BUSCOs | ≤1 gene c | |||
| Min N50 [kbp] | 53.0 b | 60.0 b | 71.7 b | 54.2 b |
| Max Duplication ratio | 1.002 b | 1.005 b | 1.015 b | 1.009 b |
Thresholds reflect data from different sources. (a): as described by Timme et al. [2]; (b): observed on in-house data, 5% and 95% quantiles of values; (c): based on in-house observation, manually chosen; (d): described in ISO norm 23418:2020 [42], (e): 5% and 95% quantile observed on publically available data from NCBI.