Table 4. Benchmark datasets.
The key features of the four empirical and one simulated dataset are summarized in this table.
| Dataset | Organism | Number of isolatesa | Epidemiologically linked isolatesb | Reference genomec | Type of dataset | Reference/Comment |
|---|---|---|---|---|---|---|
| Stone Fruit Food recall | L. monocytogenes | 31 | 28 | CFSAN023463 | Empirical | PMID: 27694232 |
| Spicy Tuna outbreak | S. enterica | 23 | 18 | CFSAN000189 | Empirical | PMID: 25995194 |
| Raw Milk Outbreak | C. jejuni | 22 | 14 | D7331 | Empirical | http://www.outbreakdatabase.com/details/hendricks-farm-and-dairy-raw-milk-2008/ |
| Sprouts Outbreak | E. coli | 10 | 3 | 2011C-3609 | Empirical | http://www.cdc.gov/ecoli/2014/o121-05-14/index.html |
| Simulated outbreak | S. enterica | 23 | 18 | CFSAN000189 | Synthetic | Simulated dataset based off the S. enterica spicy tuna outbreak tree and reference genome. |
Notes.
a
Number of Isolates: total number of isolates in the dataset.
b
Epidemiologically linked isolates: number of isolates implicated in the recall or outbreak.
c
Reference genome: suggested reference genome for SNP analysis.