Table 1.

Scores of algorithms when aligning short reads to REF-1

Algorithm	Strain			Species			Genus
	F1	Sensitivity	Precision	F1	Sensitivity	Precision	F1	Sensitivity	Precision
Pufferfish	62.12	47.27	90.58	66.04	50.25	96.29	67.92	51.68	99.05
Mora + Pufferfish	66.20	50.37	96.53	67.04	51.01	97.75	68.49	52.11	99.87
AugPatho2 + Pufferfish	66.62	50.69	97.14	66.90	50.90	97.55	68.49	52.11	99.87
Bowtie2	84.54	78.04	92.20	88.94	82.11	97.01	91.21	84.21	99.48
Mora + Bowtie2	87.59	80.86	95.54	89.22	82.37	97.32	91.48	84.46	99.79
AugPatho2 + Bowtie2	89.03	82.19	97.10	89.64	82.76	97.77	91.50	84.47	99.80
Kraken2	NA	NA	NA	88.19	83.57	93.36	92.36	87.52	97.77
Clark	59.38	55.21	64.23	91.12	84.71	98.57	92.04	85.58	99.57

Both Mora and AugPatho2 were able to improve the scores of the initial aligner, though AugPatho2 appears to have a slight systematic edge