Table 1:
Datasets used to compare primerForge to swga2.
| Dataset | Name | NCBI Accession | Group1 |
|---|---|---|---|
| plasmid2 | pcDNA | not provided | ingroup |
| plasmid2 | pLTR | not provided | outgroup |
| M. mycoides 3 | Mycoplasma mycoides subsp. mycoides str. KH3J | GCF_003034305.1 | ingroup |
| M. mycoides 3 | Mycoplasma mycoides subsp. mycoides str. B345/93 | GCF_003034275.1 | ingroup |
| M. mycoides 3 | Mycoplasma mycoides subsp. mycoides str. Gemu Goffa | GCF_003034345.1 | ingroup |
| M. mycoides 3 | Mycoplasma mycoides subsp. capri str. GM12 | GCF_900489555.1 | outgroup |
| M. mycoides 3 | Mycoplasma mycoides subsp. capri str. 80/93 | GCF_018389745.1 | outgroup |
| E. coli | Escherichia coli O157 str. 644-PT8 | GCF_001650295.1 | ingroup |
| E. coli | Escherichia coli O157 str. AR-0428 | GCF_008727175.1 | ingroup |
| E. coli | Escherichia coli O157 str. FDAARGOS_293 | GCF_002208865.2 | ingroup |
| E. coli | Escherichia coli K12 str. MG1655 | GCF_000005845 | outgroup |
| E. coli | Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 | GCF_000006945 | outgroup |
| SARS-CoV-2 | SARS-CoV-2 isolate human/USA/MA_MGH_00230/2020 | MT520374 | ingroup |
| SARS-CoV-2 | SARS-CoV-2 isolate human/USA/MA_MGH_00229/2020 | MT520263 | ingroup |
| SARS-CoV-2 | SARS-CoV-2 isolate human/USA/MA_MGH_00257/2020 | MT520479 | ingroup |
| SARS-CoV-2 | SARS-CoV-2 isolate Wuhan-Hu-1 | NC_045512 | outgroup |
1
The group indicates which set of genomes should be distinguished from each other within each dataset. The “ingroup” indicates genomes that should produce PCR products when amplified with the primer pairs identified by the software. The “outgroup” indicates genomes that should that should not produce PCR products, or should produce PCR product sizes outside a user-specified range.
2
The plasmid dataset is provided as an example in the swga2 repository.
3
The M. mycoides dataset is provided as an example in the primerForge repository.