Read mapping on de Bruijn graphs

BMC Bioinformatics

Table 4 GGMAP mapping results on simulated reads from the reference of the human chromosome 1 with default parameters

% Errors in simulated reads	Distance to optimum of BGREAT mapped reads (percentage)
	0	1	2	3	≥4
0	100	0	0	0	0
0.1	99.31	0.52	0.09	0.04	0.04
0.2	98.79	0.91	0.21	0.07	0.02
0.5	97.2	2.17	0.41	0.17	0.05
1	94.88	3.72	0.92	0.41	0.07
2	90.85	6.43	1.79	0.83	0.1

Results show the recall of GGMAP and the quality of BGREAT mapping, as represented by the “distance to optimum” value. For instance 94.88% of the reads were mapped without error, 3.72% were mapped with a distance to the optimum of one etc. Due to approximate repeats in human chromosome 1, the reported distance to optimum is an upper bound

ISSN: 1471-2105