StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities

Table 1 StrainGST was the only tool that correctly identified the known composition of a mock community

Predicted strains (approximate ANI to closest true strain)^a
Actual strain in mock community (phylogroup)	StrainGST	StrainEst	BIB
E. coli SEC470 (A)	✓	✓	E. coli K-12 GM4792, 99.24 %
E. coli UTI89 (B2)	E. coli UM146, 99.95%	E. coli UM146, 99.95%	E. coli H105, 98.49%
E. coli Sakai (E)	E. coli 149, 99.89%	E. coli 149, 99.89%	E. coli 108, 99.97%
E. coli 24377A (B1)	✓	✓	E. coli S40, 99.01%
		✘ E. coli APEC IMT5155, 99.51%	✘ S. flexneri G1663, 97.97%
		✘ E. coli RM14721, 99.44%	✘ E. coli LHM10-1, 98.12%
			✘ E. coli MSHS 133, 97.67%
			✘ S. dysenteriae 80-547, 97.71%
			✘ E. coli IMT16316, 97.39%
			✘ S. dysenteriae ATCC 12039, 97.08%

^aA check mark indicates that the exact strain was present in our database and correctly identified. A strain name indicates that the exact reference was not in the reference database, but the closest available reference was correctly identified (along with its approximate ANI to the actual strain). A strain name with an “X” indicates a false positive strain identified by the tool that was not present in the mock community. Percentages near strain names indicate approximate ANI to the closest true strain. Relative abundances for each strain are listed in Additional file 1: Table S2

ISSN: 1474-760X