Galba: genome annotation with miniprot and AUGUSTUS

BMC Bioinformatics

Table 1 F1-scores of gene predictions for the genomes of 14 different species

	Arabidopsis thaliana			Bombus terrestris			Caenorhabditis elegans			Danio rerio			Drosophila melanogaster
	Gene	Transcript	Exon	Gene	Transcript	Exon	Gene	Transcript	Exon	Gene	Transcript	Exon	Gene	Transcript	Exon
GALBA	75.32	60.09	84.82	53.89	45.19	82.82	53.51	42.28	80.99	40.16	30.07	77.53	71.07	55.05	82.74
BRAKER2	78.20	62.09	85.14	46.32	38.99	79.15	70.71	56.71	88.01	30.32	23.87	73.02	74.19	57.18	82.95
TSEBRA G+B	78.92	61.16	84.98	52.30	43.25	81.62	66.44	49.09	83.81	40.73	29.17	76.77	78.06	58.42	84.37
GALBA\(^{s}\)	71.15	57.16	84.16	49.57	41.65	81.80	47.16	38.31	78.40	32.10	25.43	75.58	68.09	52.74	81.50

	Medicago truncatula			Parasteatoda tepidariorum			Populus trichocarpa			Rhodnius prolixus			Tetraodon nigroviridis
	Gene	Transcript	Exon	Gene	Transcript	Exon	Gene	Transcript	Exon	Gene	Transcript	Exon	Gene	Transcript	Exon
GALBA	42.44	40.90	73.57	15.17	13.17	56.26	60.26	46.39	77.75	11.75	11.16	53.64	9.52	7.70	58.57
BRAKER2	46.94	46.94	74.95	20.67	18.40	63.50	67.14	56.02	82.27	13.25	12.77	54.62	9.80	8.34	58.57
TSEBRA G+B	46.93	42.35	74.01	16.51	13.63	55.51	67.09	48.65	78.18	12.75	11.36	53.03	10.45	7.92	58.55
GALBA\(^{s}\)	43.32	42.45	74.81	15.19	13.70	59.07	53.44	46.28	78.86	11.29	11.05	53.53	8.50	7.29	58.20

	Gallus gallus			Mus musculus			Solanum lycopersicum			Xenopus tropicalis			Average
	Gene	Transcript	Exon	Gene	Transcript	Exon	Gene	Transcript	Exon	Gene	Transcript	Exon	Gene	Transcript	Exon
GALBA	43.03	35.07	69.29	37.62	31.45	62.75	38.37	36.46	71.55	48.93	39.23	83.77	42.93	35.23	72.58
BRAKER2	23.92	16.29	46.50	27.80	26.96	57.39	38.36	35.91	69.33	35.76	27.84	77.91	42.05	35.42	70.41
TSEBRA G+B	50.17	35.34	83.75	50.58	31.88	79.05	39.26	35.22	70.50	49.15	37.59	82.80	47.10	36.07	73.35
GALBA\(^{s}\)	40.59	34.76	70.10	30.05	27.23	61.72	38.54	37.24	72.71	39.83	32.87	81.34	39.20	33.44	72.27

We show a direct comparison of GALBA, BRAKER2, and a combination of GALBA with BRAKER2 by TSEBRA (TSEBRA G+B) with the same input data. In addition, we provide GALBA\(^{s}\) results with one reference gene set only (labeled with \(^{s}\) in Additional file 1: Table S1)

ISSN: 1471-2105